Search

The importance of environmental reservoirs as a source from which antimicrobial resistance emerges and subsequently transferred is already established. To evaluate the role of small scale poultry slaughterhouses in resistance dissemination in Pakistan, a comparative genomic analysis of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) in the gut microbiome of broiler and household chickens (Gallus gallus domesticus) was performed. An array of 52 qPCR primers targeting the 16S rRNA gene, ARGs and MGEs was used in the experiment to analyse the abundance of selected genes in collected samples. A total of 22 ARGs and 7 MGEs were detected in all samples. The detection frequency of specific gene classes and diversity of genes was found to be higher in broiler as compared to household chicken. Sul1 was the most abundant ARG with the highest percent relative abundance (2.4%). Total percent relative abundance of ARGs in broiler chicken was found to be significantly (p < 0.05) greater than household chicken fecal samples. A significant linear correlation (R² = 0.89) was found between relative abundances of int1 and total ARGs. The clustering and correlation of selective ARGs with MGEs has implied that small scale poultry slaughterhouses can be a potential source for the dissemination of ARGs to other non-resistant environmental and/or clinical bacteria. [ABSTRACT FROM AUTHOR]

Topography of a place has a significant impact on soil characteristics that ultimately influence soil iodine levels. Lower Himalayan region (LHR) in Pakistan has a wide range of climatic and geological variations. Hence, an investigation was conducted to analyze the iodine concentration and other physicochemical properties of soils in two LHR districts, Haripur and Mansehra. Spatial analysis indicated a decrease in iodine levels in the mountainous regions in comparison to the flat portions of LHR. Soil samples obtained from different locations across Haripur had a stronger affinity for iodine due to variations in solubility and adsorption of iodine to soil clay components, which can be attributed to lower pH, higher organic matter, and a higher cation exchange capacity (CEC). In contrast to the plains of Haripur, elevated locations in the Mansehra district had decreased levels of iodine, along with a higher soil pH and reduced soil organic matter. The soil erosion and depletion of soil micronutrients in the hilly region of Mansehra may be attributed to the unfavorable soil conditions and excessive precipitation. Presence of clay, iron (Fe), and aluminum (Al) in the soil led to a rise in iodine levels. Iodine concentrations exhibited an inverse relationship with soil acidity. Study revealed a direct correlation between soil iodine levels and their cation exchange capacity (CEC) and clay content. This study aims to gather fundamental data for the chosen regions of LHR to address illnesses caused by iodine deficiency., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

This study assessed the occurrence, origins, and potential risks of emerging perfluoroalkyl acids (PFAAs) for the first time in drinking water resources of Khyber Pakhtunkhwa, Pakistan. In total, 13 perfluoroalkyl carboxylic acids (PFCAs) with carbon (C) chains C4-C18 and 4 perfluoroalkyl sulfonates (PFSAs) with C chains C4-C10 were tested in both surface and ground drinking water samples using a high-performance liquid chromatography system (HPLC) equipped with an Agilent 6460 Triple Quadrupole liquid chromatography-mass spectrometry (LC-MS) system. The concentrations of ∑PFCAs, ∑PFSAs, and ∑PFAAs in drinking water ranged from 1.46 to 72.85, 0.30-8.03, and 1.76-80.88 ng/L, respectively. Perfluorobutanoic acid (PFBA), perfluorohexanoic acid (PFHxA), and perfluoropentanoic acid (PFPeA) were the dominant analytes in surface water followed by ground water, while the concentration of perfluorobutane sulfonate (PFBS), perfluorooctanoic acid (PFOA), perfluoroheptanoic acid (PFHpA), perfluorooctane sulfonate (PFOS), perfluorohexane sulfonate (PFHxS), perfluorononanoic acid (PFNA), perfluorodecanoic acid (PFDA), perfluoroundecanoic acid (PFUnDA), and perfluorododecanoic acid (PFDoDA) were greater than long-chain PFOA and PFOS. The correlation statistics, which showed a strong correlation (p < 0.05) between the PFAA analytes, potentially indicated the fate of PFAAs in the area's drinking water sources, whereas the hierarchical cluster analysis (HCA) and principal component analysis (PCA) statistics identified industrial, domestic, agricultural, and commercial applications as potential point and non-point sources of PFAA contamination in the area. From risk perspectives, the overall PFAA toxicity in water resources was within the ecological health risk thresholds, where for the human population the hazard quotient (HQ) values of individual PFAAs were < 1, indicating no risk from the drinking water sources; however, the hazard index (HI) from the ∑PFAAs should not be underestimated, as it may significantly result in potential chronic toxicity to exposed adults, followed by children., Competing Interests: Declaration of competing interest The authors have no relevant financial or non-financial interests to disclose., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

The emergence of plasmid-mediated tigecycline resistance gene tet(X4) among clinically relevant bacteria has promoted significant concerns, as tigecycline is considered a last-resort drug against serious infections caused by multidrug-resistant bacteria. We herein focused on the isolation and molecular characterization of tet(X4)-positive Klebsiella pneumoniae (K. pneumoniae) and Escherichia coli (E. coli) in wild bird populations with anthropogenic interaction in Faisalabad, Pakistan. A total of 150 birds including black kites (Milvus migrans) and house crows (Corvus splendens) were screened for the presence of tigecycline resistance K. pneumoniae and E. coli. We found two K. pneumoniae and one E. coli isolate carrying tet(X4) originating from black kites. A combination of short- and long-read sequencing strategies showed that tet(X4) was located on a broad host range IncFII plasmid family in K. pneumoniae isolates whereas on an IncFII-IncFIB hybrid plasmid in E. coli. We also found an integrative and conjugative element ICEKp2 in K. pneumoniae isolate KP8336. We demonstrate the first description of tet(X4) gene in the WHO critical-priority pathogen K. pneumoniae among wild birds. The convergence of tet(X4) and virulence associated ICEKp2 in a wild bird with known anthropogenic contact should be further investigated to evaluate the potential epidemiological implications. The potential risk of global transmission of tet(X4)-positive K. pneumoniae and E. coli warrant comprehensive evaluation and emphasizes the need for effective mitigation strategies to reduce anthropogenic-driven dissemination of AMR in the environment., (© 2024. The Author(s).)

Background: Genetic studies play a significant role in understanding the underlying risk factors of breast cancer. Polymorphism in the tumor suppressor gene TP 53, CDH1 and ATM genes are found to increase susceptibility for breast cancer globally., Objective: This study aimed to identify/analyze the contribution of genetic polymorphisms in the breast cancer candidate genes ATM, TP53 and CDH1 that may be associated with familial breast cancer risk in the Khyber Pakhtunkhwa population., Subjects and Methods: In the present case-control study, Whole Exome Sequencing (WES) of the 100 breast cancer patients and 100 ethnic controls were performed for the selected genes in the target population., Results: Of the studied variants rs3743674 of the CDH1 gene (crude P=0.014 and adjusted p=0.000) evident significant association with breast cancer in Pakistani Pashtun population. Whereas TP53rs1042522 (crude P=0.251 and adjusted P=0.851) and ATM rs659243 (crude p=0.256 and adjusted p=0.975) showed no or negative association with breast cancer in study population., Conclusion: The present study demonstrates that CDH1rs3743674 polymorphism is associated with elevated breast cancer risk in the Pashtun ethic population of Khyber Pakhtunkhwa., (© 2022 Rahim A et al.)

This study aimed to characterize the whole genome of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) isolated from an oropharyngeal swab specimen of a Pashtun Pakistani patient using next-generation sequencing. Upon comparing the SARS-CoV2 genome to the reference genome, a total of 10 genetic variants were identified. Among the 10 genetic variants, 1 missense mutation (c.1139A > G, p.Lys292Glu) in the Open Reading Frame 1ab (ORF1ab) positioned at 112 in the non-structural protein 2 (NSP2) was found to be unique. Phylogenetic analysis (n = 84) revealed that the current SARS-CoV2 genome was closely clustered with 8 Pakistani strains belonging to Punjab, Federal Capital, Azad Jammu and Kashmir (AJK), and Khyber Pakhtunkhwa (KP). In addition, the current SARS-CoV2 genome was very similar to the genome of SARS-CoV2 reported from Guam, Taiwan, India, the USA, and France. Overall, this study reports a slight mismatch in the SARS-CoV2 genome, indicating the presence of a single unique missense mutation. However, phylogenetic analysis revealed that the current SARS-CoV2 genome was closely clustered with 8 other Pakistani strains., (© 2021. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Aims: To identify the changes in cardiovascular disease presentation, emergency room triage and inpatient diagnostic and therapeutic pathways., Methods: We conducted a retrospective cohort study at the Aga Khan University Hospital, Karachi. We collected data for patients presenting to the emergency department with cardiovascular symptoms between March-July 2019 (pre-COVID period) and March-July 2020 (COVID period). The comparison was made to quantify the differences in demographics, clinical characteristics, admission, diagnostic and therapeutic procedures, and in-hospital mortality between the two periods., Results: Of 2976 patients presenting with cardiac complaints to the emergency department (ED), 2041(69%) patients presented during the pre-COVID period, and 935 (31%) patients presented during the COVID period. There was significant reduction in acute coronary syndrome (ACS) (8% [95% CI 4-11], p < 0.001) and heart failure (↓6% [95% CI 3-8], p < 0.001). A striking surge was noted in Type II Myocardial injury (↑18% [95% CI 20-15], p < 0.001) during the pandemic. There was reduction in cardiovascular admissions (coronary care unit p < 0.01, coronary step-down unit p = 0.03), cardiovascular imaging (p < 0.001), and procedures (percutaneous coronary intervention p = 0.04 and coronary angiography p = 0.02). No significant difference was noted in mortality (4.7% vs. 3.7%). The percentage of patients presenting from rural areas declined significantly during the COVID period (18% vs. 14%, p = 0.01). In the subgroup analysis of sex, we noticed a falling trend of intervention performed in females during the COVID period (8.2% male vs. 3.3 % female)., Conclusions: This study shows a significant decline in patients presenting with Type I myocardial infarction (MI) and a decrease in cardiovascular imaging and procedures during the COVID period. There was a significant increase noted in Type II MI., Competing Interests: The authors have no competing interests to declare., (Copyright: © 2021 The Author(s).)

A high prevalence of multidrug-resistant (MDR) pathogens has been reported in adult and pediatric populations of Pakistan. However, data describing the effect of MDR microbes on the gut microbiota is scarce. We designed a cross-sectional pediatric study to investigate the effect of MDR microbes' infection on the gut microbiome and its resistome of children using high-throughput next-generation sequencing (NGS). A cross-sectional study was conducted at a tertiary health care hospital in Peshawar Pakistan, between 5 September 2019 to 15 February 2020. Pediatric patients with acute gastroenteritis (n = 200) were enrolled. All the enrolled pediatric patients underwent initial antimicrobial resistance (AMR) screening using the disk diffusion method. Children with MDR infections were identified and selected for gut microbiome and its resistome profiling using NGS. Out of 200 enrolled pediatric patients, 80 (40%) were found infected with MDR diarrheagenic Enterobacteriaceae consisting of 50 (62.5%) infections caused by extended-spectrum beta-lactamase (ESBL) producing E. coli while 30 (37.5%) by MDR Enterobacter specie. A total of 63 and 17 antibiotic-resistant genes (ARGs) conferring resistance to 7 and 5 classes of antibiotics were identified in the resistomes of MDR diarrheagenic Enterobacteriaceae infected and healthy children, respectively. NGS-based gut microbial profiling of MDR Enterobacter spp ., ESBL producing E. coli infected pediatric patients and healthy controls revealed the predominance of Proteobacteria and Actinobacteria , respectively. An increased abundance of several pathogenic gram-negative bacteria namely E. coli, Enterobacter cloacae , and Salmonella enterica was observed in the gut microbiota of children infected with MDR bacterial infections than that of the healthy controls. This work indicates that children with MDR infections have reduced microbial diversity and enriched ARGs than healthy controls. The emergence of MDR bacterial strains and their association with gut dysbiosis needs immediate attention to regulate antibiotics usage in Pakistani children.

Background: Cancer patients, particularly those on active anticancer treatment, are reportedly at a high risk of severe coronavirus disease 2019 (COVID-19) infection and death. This study aimed to describe the clinical characteristics and outcomes of patients diagnosed with COVID-19 whilst on anticancer treatment in a developing country., Methods: This is a retrospective observational study of all adult cancer patients at Shaukat Khanum Memorial Cancer Hospital and Research Centre, Pakistan, from March 15, 2020 to July 10, 2020, diagnosed with COVID-19 within 4 weeks of receiving anticancer treatment, where a purposive sampling was performed. Cancer patients who did not receive anticancer treatment and clinical or radiological diagnosis of COVID-19 without a positive reverse transcription-polymerase chain reaction (RT-PCR) test were excluded. The primary endpoint was all-cause mortality after 30 days of COVID-19 test. Data was analyzed with SPSS version 23 (SPSS Inc., Chicago, IL, USA). Categorical parameters were computed using chi-square test, keeping p value < 0.05 as significant., Results: A total of 201 cancer patients with COVID-19 were analyzed. The median age of patients was 45 (18-78) years. Mild symptoms were present in 162 (80.6%) patients, whereas severe symptoms were present in 39 (19.4%) patients. The risk of death was statistically significant (p < .05) amongst patients with age greater than 50 years, metastatic disease, and ongoing palliative anticancer treatment. Anticancer treatment (chemotherapy, radiotherapy, hormonal therapy, targeted therapy, and surgery) received within preceding 4 weeks had no statistically significant (p > .05) impact on mortality., Conclusions: In cancer patients with COVID-19, mortality appears to be principally driven by age, advanced stage of the disease, and palliative intent of cancer treatment. We did not identify evidence that cancer patients on chemotherapy are at significant risk of mortality from COVID-19 correlating to those not on chemotherapy., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 King Faisal Specialist Hospital & Research Centre. Published by Elsevier Ltd. All rights reserved.)

The ongoing COVID-19 pandemic is caused by SARs-CoV-2. The virus is transmitted from person to person through droplet infections i.e. when infected person is in close contact with another person. In January 2020, first report of detection of SARS-CoV-2 in faeces, has made it clear that human wastewater might contain this virus. This may illustrate the probability of environmentally facilitated transmission, mainly the sewage, however, environmental conditions that could facilitate faecal oral transmission is not yet clear. We used existing Pakistan polio environment surveillance network to investigate presence of SARs-CoV-2 using three commercially available kits and E-Gene detection published assay for surety and confirmatory of positivity. A Two-phase separation method is used for sample clarification and concentration. An additional high-speed centrifugation (14000Xg for 30 min) step was introduced, prior RNA extraction, to increase viral RNA yield resulting a decrease in Cq value. A total of 78 wastewater samples collected from 38 districts across Pakistan, 74 wastewater samples from existing polio environment surveillance sites, 3 from drains of COVID-19 infected areas and 1 from COVID 19 quarantine center drainage, were tested for presence of SARs-CoV-2. 21 wastewater samples (27%) from 13 districts turned to be positive on RT-qPCR. SARs-COV-2 RNA positive samples from areas with COVID 19 patients and quarantine center strengthen the findings and use of wastewater surveillance in future. Furthermore, sequence data of partial ORF 1a generated from COVID 19 patient quarantine center drainage sample also reinforce our findings that SARs-CoV-2 can be detected in wastewater. This study finding indicates that SARs-CoV-2 detection through wastewater surveillance has an epidemiologic potential that can be used as supplementary system to monitor viral tracking and circulation in cities with lower COVID-19 testing capacity or heavily populated areas where door-to-door tracing may not be possible. However, attention is needed on virus concentration and detection assay to increase the sensitivity. Development of highly sensitive assay will be an indicator for virus monitoring and to provide early warning signs., Competing Interests: The authors have declared that no competing interests exist.

Genome-wide association studies (GWAS) have identified multiple type 2 diabetes (T2D) loci, mostly among populations of European descent. There is a high prevalence of T2D among Pakistanis. Both genetic and environmental factors may be responsible for this high prevalence. In order to understand the shared genetic basis of T2D among Pakistanis and Europeans, we examined 77 genome-wide significant variants previously implicated among European populations. We genotyped 77 single-nucleotide polymorphisms (SNPs) by iPLEX® Gold or TaqMan® assays in a case-control sample of 1,683 individuals. Association analysis was performed using logistic regression. A total of 16 SNPs (TCF7L2/rs7903146, GLIS3/rs7041847, CHCHD9/rs13292136, PLEKHA1/rs2292626, FTO/rs9936385, CDKAL1/rs7756992, KCNJ11/rs5215, LOC105372155/rs12970134, KCNQ1/rs163182, CTRB1/rs7202877, ST6GAL1/rs16861329, ADAMTS9-AS2/rs6795735, LOC105370275/rs1359790, C5orf67/rs459193, ZBED3-AS1/rs6878122 and UBE2E2/rs7612463) showed statistically significant associations after controlling for the false discovery rate. While KCNQ1/rs163182 and ZBED3-AS1/rs6878122 showed opposite allelic effects, the remaining significant SNPs had the same allelic effects as reported previously. Our data indicate that a selected number of T2D loci previously identified among populations of European descent also affect the risk of T2D in the Pakistani population., (Copyright © 2021. Published by Elsevier B.V.)

Background: Emerging evidence suggests that the South Asian (SA) population has an increased rate of in-stent stenosis (ISR) after percutaneous coronary intervention (PCI) when compared with other ethnicities. Drug-eluting balloons (DEBs) have emerged as a viable option for the treatment of ISR. However, data describing the outcomes of DEB-PCI in the SA population are limited. Since the magnitude of the problem is high in the SA population, it is essential to evaluate the outcomes of DEB-PCI for ISR., Methods: In this cohort study, we investigated the incidence of target-lesion revascularization (TLR) and major adverse cardiac event (MACE) after PCI with DEB for ISR at 1 year and at long-term follow-up in Pakistani patients. From January 2010 to January 2019, a total of 147 ISR lesions in 112 patients were treated with DEB-PCI at our center., Results: The incidence of clinically driven TLR and MACE after a 1-year follow-up was 15.2% and 16.1%, respectively. At mean long-term follow-up of 2.73 ± 2.14 years, the TLR and MACE rates were 26.8% and 35.7%, respectively. The major predictors for TLR were diffuse and occlusive ISR types, DEB for a recurrent restenosis lesion, and the presence of ≥3 traditional cardiovascular disease risk factors., Conclusions: The high rates of follow-up TLR and MACE reported in this study may suggest that the outcomes of DEB-PCI for ISR in the SA population may be unsatisfactory. With the increasing use of DEBs, it is imperative to further investigate DEB-PCI outcomes in the SA population with large, prospective studies.

Antibiotics discovery was a significant breakthrough in the field of therapeutic medicines, but the over (mis)use of such antibiotics (in parallel) caused the increasing number of resistant bacterial species at an ever-higher rate. This study was thus devised to assess the multi-drug resistant bacteria present in sanitation-related facilities in human workplaces. In this regard, samples were collected from different gender, location, and source-based facilities, and subsequent antibiotic sensitivity testing was performed on isolated bacterial strains. Four classes of the most commonly used antibiotics i.e., β-lactam, Aminoglycosides, Macrolides, and Sulphonamides, were evaluated against the isolated bacteria. The antibiotic resistance profile of different (70) bacterial strains showed that the antibiotic resistance-based clusters also followed the grouping based on their isolation sources, mainly the gender. Twenty-three bacterial strains were further selected for their 16s rRNA gene based molecular identification and for phylogenetic analysis to evaluate the taxonomic evolution of antibiotic resistant bacteria (ARB). Moreover, the bacterial resistance to Sulphonamides and beta lactam was observed to be the most and to Aminoglycosides and macrolides as the least. Plasmid curing was also performed for multidrug resistant (MDR) bacterial strains, which significantly abolished the resistance potential of bacterial strains for different antibiotics. These curing results suggested that the antibiotic resistance determinants in these purified bacterial strains are present on respective plasmids. Altogether, the data suggested that the human workplaces are the hotspot for the prevalence of MDR bacteria and thus may serve as the source of horizontal gene transfer and further transmission to other environments., Competing Interests: The authors have declared that no competing interests exist.

β-Thalassemia (β-thal) is a common monogenic disease with ethnic-specific mutations on the HBB gene throughout the world. The reported mutations either reduce the expression or completely inactivate the HBB gene. In Pakistan, the prevalence of β-thal is high due to consanguineous marriages. Accurate identification of mutations in carriers is imperative for prevention of β-thal in subsequent generations. To overcome the limitations of traditional testing methods for β-thal, a next-generation sequencing (NGS)-based diagnostic test was designed and validated by sequencing the entire HBB gene. The primer set covering the entire HBB gene was designed and validated in a Pashtun β-thalassemic family. The polymerase chain reaction (PCR) product was sequenced using an Illumina MiSeq platform. A homozygous pathogenic insertion of A>AC/AC (rs35699606) was detected in an affected member of the family, while unaffected members were heterozygous for it. In addition, all family members were homozygous for the synonymous variant, A>G/G (rs713040), except the father who was heterozygous for it. We sequenced the entire HBB gene using the NGS-based test, which is highly sensitive, robust and specific for the diagnosis and screening of β-thal in Pakistan, especially for families practicing consanguineous marriages.

Genome-wide association studies (GWAS) of coronary artery disease (CAD) have revealed multiple genetic risk loci. We assessed the association of 47 genome-wide significant single-nucleotide polymorphisms (SNPs) at 43 CAD loci with coronary stenosis in a Pakistani sample comprising 663 clinically ascertained and angiographically confirmed cases. Genotypes were determined using the iPLEX Gold technology. All statistical analyses were performed using R software. Linkage disequilibrium (LD) between significant SNPs was determined using SNAP web portal, and functional annotation of SNPs was performed using the RegulomeDB and Genotype-Tissue Expression (GTEx) databases. Genotyping comparison was made between cases with severe stenosis (≥70%) and mild/minimal stenosis (<30%). Five SNPs demonstrated significant associations: three with additive genetic models PLG /rs4252120 ( p = 0.0078), KIAA1462 /rs2505083 ( p = 0.005), and SLC22A3 /rs2048327 ( p = 0.045) and two with recessive models SORT1 /rs602633 ( p = 0.005) and UBE2Z /rs46522 ( p = 0.03). PLG /rs4252120 was in LD with two functional PLG variants (rs4252126 and rs4252135), each with a RegulomeDB score of 1f. Likewise, KIAA1462 /rs2505083 was in LD with a functional SNP, KIAA1462 /rs3739998, having a RegulomeDB score of 2b. In the GTEx database, KIAA1462 /rs2505083, SLC22A3 /rs2048327, SORT1 /rs602633, and UBE2Z /rs46522 SNPs were found to be expression quantitative trait loci (eQTLs) in CAD-associated tissues. In conclusion, five genome-wide significant SNPs previously reported in European GWAS were replicated in the Pakistani sample. Further association studies on larger non-European populations are needed to understand the worldwide genetic architecture of CAD., Competing Interests: The authors declare that they have no conflicts of interest., (Copyright © 2020 Asma Naseer Cheema et al.)

The present study was conducted to investigate the concentrations of potential toxic metals (PTMs) in agricultural soil (n = 25) and their bioaccumulation in wheat crop (n = 25) collected from alongside the Kurram River, Pakistan. The highest concentrations of Cd, Cr, Cu, Fe, Mn, Ni, Pb, and Zn in soil samples were 0.16, 19.5, 14.7, 46.5, 13.5, 14.5, 14.0, and 19.7 mg kg -1 , respectively. In the edible tissues of cultivated wheat crop, the highest concentrations of Cd, Cr, Cu, Fe, Mn, Ni, Pb, and Zn were 0.15, 10.00, 8.75, 22.25, 11.00, 11.25, 10.50, and 7.50 mg kg -1 , respectively. The selected PTM concentrations in soil samples were observed within their respective permissible limits set by the Food and Agriculture Organization (FAO) and State Environmental Protection Administration (SEPA) China, while in wheat crops, the Cr and Pb concentrations were above the permissible limits of both FAO and SEPA China. The results showed that the orders of PTMs were Fe > Zn > Cr > Cu > Ni > Pb > Mn in soil and Fe > Ni > Mn > Pb > Cr > Cu > Zn in wheat. The highest PTM concentrations were reported in the sample collected near dumping sites. The results of different soil pollution indices including geo-accumulation index (Igeo), contamination factor (CF), and enrichment factor (EF) indicated that the soil of the study area was moderately to severely contaminated. The ADI values of wheat crops were less than 1, while the HQ varied among different PTMs with the highest value of 2.118 for Pb, and the lowest for Zn (0.007). The results indicated that anthropogenic intervention has made a substantial contribution to soil contamination with PTMs and subsequent uptake by wheat, which may exert potential human health risk.

The present study was conducted to explore the farmer's perception regarding constraints faced in adoption of dairy farming practices in Sindh province of Pakistan. The data were collected from 133 project dairy farmers of Pakistan Dairy Development Company (PDDC) and 133 non-PDDC dairy farmers. The constraints were measured with three-point continuum scale. The survey results revealed that on overall basis, technical, financial, and physical constraints, viz., poor conception rate of artificial insemination (AI) in buffaloes, high price of concentrates, high cost of treatment, etc. received higher scores for both groups (PDDC and non-PDDC farmers). In contrast, overall mean scores were relatively low for knowledge (lack of knowledge about proper time of AI/natural service, heat detection, disease control, scientific housing, clean milk production), skills (lack of technical skills regarding fodder conservation and preparation of balanced ration), and lack of financial support by government, etc.; recorded as severe constraints with higher scores for non-PDDC farmers as compared to PDDC farmers. These results indicate that augmenting extension services through PDDC on training and technical know-how is essential to overcome constraints of adoption by farmers who never adopted the practices, while technical, financial, and physical support to farmers are critical for a wider scale, sustained adoption of livestock practices.

Background: Antimicrobial resistance (AMR) is an emerging threat to public health worldwide. A significant evidence has suggested that the knowledge and attitude trends among the community, pharmacists and physicians can play a critical role in managing the ever increasing threat of AMR., Methods: A cross-sectional survey was performed using three specific self-administered questionnaires for community members, pharmacists/pharmacy owners and physicians on a randomly selected sample population of 473, 424 and 308 respectively. Bivariate and multivariate logistic regression and Pearson chi-square tests were performed during data analysis., Result: A response rate of 81.2% ( n  = 385), 37.7% ( n  = 160) and 53.9% ( n  = 166) was achieved for general community, pharmacists/pharmacy owners and physicians respectively. More than half of the community participants (55.6%; n  = 214) possess poor knowledge of AMR. Furthermore, knowledge and attitude of the community participants were also found to be significantly correlated (r 2  = 0.02) with each other. In 90.6% ( n  = 145) of the pharmacies included in the survey, a qualified pharmacist was not present at the time of the operations. Only 36.9% physicians ( n  = 60) knew about the environmental route of dissemination of AMR. Majority of the physicians agreed that AMR is a global problem and also recognize the need for initiating AMR stewardship programs., Conclusion: Our study will provide effective assessment and potential insights in designing tri-faceted interventions for rationalizing antibiotics consumption thus controlling the development and dissemination of AMR., Competing Interests: A consent was taken from the participants of the study before giving them questionnaire.The authors declare that they have no competing interests.Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

In present study, the volatilization of arsenic (As), cadmium (Cd), mercury (Hg) and lead (Pb) by the burning of coal samples in the electric furnace was evaluated. The coal samples were obtained from different blocks of newly developed Thar coal field, Pakistan. The replicate coal samples were heated/burned in an electric furnace at laboratory scale for three temperature intervals (200, 400 and 900 °C). The ash obtained after each temperature intervals were analyzed for selected toxic elements. The resulted data indicated that the total contents of As, Cd, and Pb in coal samples of block X and XI were found in the range of 16.8-18.5, 4.21-4.72, and 14.2-18.8 mg/kg, respectively. Whereas, 67.8-79.7%, 34.3-36.8% and 9.89-10.8% of As, Cd, and Pb, respectively, were volatized out after combustion of coal samples at 900 °C. The total contents of Hg in selected coal samples of block X and XI were observed in the range of 0.985-1.46 and 0.992-1.41 mg/kg, respectively. The contents of Hg volatilized out via burning in a furnace at 200 °C and 400 °C, were observed in the range of 32.0-36.5% and >91.0% of its total contents, respectively, whereas at 900 °C, it was not detected in ash. The partitioning and mobility of studied toxic elements in residue termed as (laboratory made ash) obtained after burning at 900 °C, was carried out by three-step sequential extraction scheme. The resulted data of present study will give a better knowledge about the quality of coal and its burning product, which may help to take measure to reduce the adverse effects on the environment in future., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

A simple vortex-assisted modified dispersive liquid-liquid microextraction procedure is proposed for the enrichment of cadmium (Cd+2) in surface (stored rainwater) and groundwater of the Tharparkar district in Pakistan, before analysis by flame atomic absorption spectrometry. Ammonium pyrrolidinedithiocarbamate was used as a ligand to make a hydrophobic complex of Cd+2, which was extracted in an ionic liquid (1-butyl-3-methylimidazolium hexafluorophosphate), and the nonionic surfactant Triton X-114 was applied as a dispersing medium. The contents of tubes were shaken for different time intervals on a vortex mixer to enhance extraction efficiency. A multivariate strategy was used to simultaneously evaluate seven factors including, concentration of the complexing reagent, pH, amounts of ionic liquid and Triton X-114, vortex shaking time, centrifugation time and extracting solution for their influence on the percentage recovery of the analyte. The important variables were further optimized by central composite design. The preconcentration factor and LOD were observed as 76.9 and 0.048 µg/L, respectively. The Certified Reference Material SRM1643e was used to check the validity of the developed method, and the RSD was found to be 4.02%. The proposed technique was successfully applied for the enrichment of Cd+2 in groundwater and surface water samples from the southeastern part of Pakistan. The observed results revealed that the concentration of Cd+2 in groundwater was higher than the World Health Organization recommended value of 3 µg/L for drinking water. For adults weighing approximately 60 kg, consumption of groundwater for drinking and other domestic purposes would provide levels of Cd+2 that are 2- to 3-fold higher than the provisional maximum tolerable daily intake.

Objective: To elucidate the genetic risk and role of alpha-synuclein gene in the pathogenesis of Parkinson's disease in Pakistani population., Methods: This case-control study was conducted at Institute of Biomedical and Genetic Engineering (IBGE), Islamabad from May 2013 to May 2016, and comprised patients with Parkinson's disease and their ethnically-matched healthy controls. Allele-specific polymerase chain reaction was used for screening of three pathogenic single nucleotide polymorphisms in alpha-synuclein gene. Moreover, 20% samples were randomly selected for bidirectional Sanger sequencing to confirm the results. SPSS 13 was used for data analysis., Results: Of the 374 participants, 174(46.5%) were patients and 200(53.5%) were controls. The mean age for the onset of the disease was 55±13 years. No polymorphism was observed for rs104893875(G>A), rs104893877(G>A) and rs104893878(C>G) in alpha-synuclein gene in samples of patients and controls., Conclusions: Alpha-synuclein gene mutations might not be relevant to all the populations in causing Parkinson's disease.

In the present study, an indigenous biosorbent (leaves of Tecomella undulata) was used for the simultaneous removal of inorganic arsenic species (As(III) and As(V)) from the stored rainwater in Tharparkar, Pakistan. The Plackett-Burman experimental design was used as a multivariate strategy for the evaluation of the effects of six factors/variables on the biosorption of inorganic arsenic species, simultaneously. Central composite design (CCD) was used to found the optimum values of significant factors for the removal of As(III) and As(V). Initial concentrations of both inorganic As species, pH, biosorbent dose, and contact time were selected as independent factors in CCD, while the adsorption capacity (q e) was considered as a response function. The separation of inorganic As species in water samples before and after biosorption was carried out by cloud point and solid-phase extraction methods. Theoretical values of pH, concentration of analytes, biosorbent dose, and contact time were calculated by quadratic equation for 100 % biosorption of both inorganic As species in aqueous media. Experimental data were modeled by Langmuir and Freundlich isotherms. Thermodynamic and kinetic study indicated that the biosorption of As(III) and As(V) was followed by pseudo second order. It was concluded that the indigenous biosorbent material efficiently and simultaneously removed both As species in the range of 70.8 to 98.5 % of total contents in studied ground water samples. Graphical abstract Optimizing the significant varable by central 2(3) + star orthogonal composite design.

In present study, the ground water at different aquifers was evaluated for physicochemical parameters, iron, total arsenic, total inorganic arsenic and arsenic species (arsenite and arsenate). The samples of groundwater were collected at different depths, first aquifer (AQ1) 50-60 m, second aquifer (AQ2) 100-120 m, and third aquifer (AQ3) 200-250 m of Thar coalfield, Pakistan. Total inorganic arsenic was determined by solid phase extraction using titanium dioxide as an adsorbent. The arsenite was determined by cloud point extraction using ammonium pyrrolidinedithiocarbamate as a chelating reagent, and resulted complex was extracted by Triton X-114. The resulted data of groundwater were reported in terms of basic statistical parameters, principal component, and cluster analysis. The resulted data indicated that physicochemical parameters of groundwater of different aquifers were exceeded the World Health Organization provisional guideline for drinking water except pH and SO4(2-). The positive correlation was observed between arsenic species and physicochemical parameters of groundwater except F(-) and K(+), which might be caused by geochemical minerals. Results of cluster analysis indicated that groundwater samples of AQ1 was highly contaminated with arsenic species as compared to AQ2 and AQ3 (p > 0.05).

Genetic variation in lipid regulatory genes, particularly APOE, significantly influences the risk of coronary artery disease (CAD). This study aimed to assess the association between APOE polymorphism and angiographically assessed coronary stenosis in Pakistani population. A total of 695 subjects (22.3% female, mean age = 54 ± 11 years) presenting with chest pain were enrolled after obtaining written informed consent. CAD stenosis/extent was assessed by angiography. Patients were classified as having severe stenosis (≥ 70%), moderate stenosis (30-69%), and mild stenosis (<30%). CAD patients with ≥ 70% stenosis (n = 491) were further categorized based on possessing one, two, or three vessel diseases to assess the disease extent. Genomic DNA from leukocytes was isolated with DNA purification kit (Qiagen) and APOE polymorphisms (E2/E3/E4) were determined using TaqMan assays. Six hundred and seventy-two of 695 subjects were successfully genotyped. The frequency of APOE∗4 carriers (3/4 and 4/4 genotypes) was significantly higher in severe stenosis group (≥ 70%) as compared to mild group (<30%) (22.8% versus 13.01%; P = 0.01). In multiple regression, the odds ratio for APOE∗4 carriers to develop ≥ 70% stenosis was 2.16 (95% CI: 1.29-3.79; P < 0.005). In conclusion, the presence of APOE∗4 allele is a significant risk factor to develop severe coronary stenosis (>70%) among Pakistanis.

Scientific progress is a significant basis for change in public-health policy and practice, but the field also invests in value-laden concepts and responds daily to sociopolitical, cultural and evaluative concerns. The concepts that drive much of public-health practice are shaped by the collective and individual mores that define social systems. This paper seeks to describe the ethics processes in play when public-health mechanisms are established in low- and middle-income countries, by focusing on two cases where ethics played a crucial role in producing positive institutional change in public-health policy. First, we introduce an overview of the relationship between ethics and public health; second, we provide a conceptual framework for the ethical analysis of health system events, noting how this approach might enhance the power of existing frameworks; and third, we demonstrate the interplay of these frameworks through the analysis of a programme to enhance road safety in Malaysia and an initiative to establish a national ethics committee in Pakistan. We conclude that, while ethics are gradually being integrated into public-health policy decisions in many developing health systems, ethical analysis is often implicit and undervalued. This paper highlights the need to analyse public-health decision-making from an ethical perspective.

Background: Gallstone disease is common in women. Many patients undergoing abdominal ultrasound for gynaecological diseases are found to have gallstones. This study was done to see the results of combined abdominal hysterectomy, mini-cholecystectomy and appendicectomy in a set up lacking facilities of laparoscopic surgery., Methods: This prospective study was conducted in Ayub Teaching Hospital, Iltaf Hospital and Shahina Jamil Trust Hospital of Abbottabad from August 1998 to July 2004. All patients undergoing combined abdominal hysterectomy and mini-cholecystectomy were exclusively studied with reference to following variables. Age, Weight, Parity, Co-morbid conditions, peri-operative and post-operative complications, blood transfusion, hospital stay and mean extra time for mini-cholecystectomy and appendicectomy after abdominal hysterectomy., Results: There were 25 patients in the study group. The ages ranged from 35-50 years. Mean weight was 65 Kg. There were no operative complications. Mild postoperative complications occurred in 7(28%) patients. Mean extra time for cholecystectomy was 25 minutes. Mean hospital stay was 9 days., Conclusions: In selected women, combined abdominal hysterectomy, cholecystectomy and appendicectomy is a safe, feasible and cost effective procedure.

Background: Deep seated lesions of the brain cannot be approached by conventional neurosurgical approach stereotactic system offers minimally invasive and accurate approach to such lesions. This study was carried out with an objective to determine the safety, efficacy and diagnostic yield of stereotactic biopsies of brain lesions using Brown-Roberts-Wells (BRW) system., Methods: This study was carried out in patients with intracranial lesions at Ayub teaching hospital Abbottabad from September 1999 to October 2003. Suitable patients with intra cranial lesions underwent computerized stereo tactic biopsy with BRW system. Tissue specimens were analyzed in histopathology department of the Ayub Medical College and results were obtained. Data was analyzed via computer software SPSS 8.0 version for windows., Results: Fifteen patients were selected for stereotactic brain biopsy. Age ranged from 15 years to 54 years. Among them 09 (60%) were male and 06 (40%) were female patients. Out come of the procedure was highly promising in terms of safety and positive diagnostic yield in 14 patients (93.3%), and histopathalogical validity of results (93.3%). Only one patient suffered mild neurological deficit (6.7%), one patient had inconclusive tissue diagnosis and invalid result (6.7%). biopsy proven lesion was astrocytoma in 04 patients (26.7%), anaplastic astrocytoma in 04 (26.7%), gliomatosis in 02 (13.3%), tuberculomas in 03 (20.0%). metastatic adenocarcinomas in 01 (6.7%) and lymphoma in 01(6.7%)., Conclusions: We conclude that computerized stereotactic brain biopsy is safe and effective procedure with a high diagnostic yield at our center.

Background: Early diagnosis and management of brain tumors is important to reduce morbidity and mortality. The objective of this study was to calculate frequency of different types of brain tumors in patients operated and managed at Ayub Teaching Hospital, Abbottabad., Methods: This study was carried out at Neurosurgical Department of Ayub Teaching hospital, Abbottabad from September 1999 to October 2003. Records of patients who consented for surgery after CT scan evidence of brain tumors, which were proved on biopsy later on, were included in the study. The tissue biopsy was taken by open craniotomy or by computerized stereotactic method. Pattern of different brain tumors was studied during this period., Results: Our study revealed predominantly tumors arising from neuroepithelium (49.2%) while tumors arising from meninges were relatively low (23.3%). Nerve sheath tumors (4.2%), germ cell tumors, mal-developmental origin (2.5%), blood vessel tumors (5.8%) and miscellaneous tumors (6.6%) were found relatively in a very low frequency., Conclusion: Evaluation of brain tumor frequency will help in future management plan that may be in the form of open craniotomy, stereo tactic radiosurgery, whole brain radiotherapy or gamma knife surgery.

Three hundred random sputum samples were collected for analysis from cases of mild to severe respiratory infections and screened for Legionella pneumophila by both the culture method and also the direct fluorescent antigen test. In one third of the cases, blood specimen was also collected and screened for Legionella serum antibodies. With the direct fluorescent test it was possible to identify Legionella in 9% of the samples while the culture gave positive results in 4.3% of cases. Diagnostic antibody titers (1:256) were obtained in 12% of the samples while another 12% cases showed serum antibody titers of 1:64 to 1:128. In Pakistan where antibiotics are used extensively, the direct fluorescent examination of sputum samples gives more accurate diagnosis of Legionella cases than the culture method.