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There have been 6,566,610 fatalities and 626,337,158 reported cases of COVID-19 worldwide. Pakistan presently has over 1,573,922 confirmed cases and 30,625 deaths. A survey-based study was performed from January to September 2022 among different university communities to find out their KAP level. Data was collected in Google Forms through a questionnaire. The Independent t-test, Multinomial regressions, and Non-parametric Mann-Whitney test were used to assess the level of significance (p-value ≤0.05). 317 out of 605 participants were male (52.5 %), the majority of participants were 15-29 years old (72.7 %), unmarried/divorced (71.6 %), have no children (82.1 %), residing in the urban area (54.9 %) and possess a college/university degree (59.5 %). The majority of participants correctly answered five out of six knowledge questions (M = 4.96, SD = 1.03) and correctly identified the primary symptoms of COVID-19 (94.4 %) along with the proper identification of mode of transmission (95.2 %) while 1.8% wrongly replied and 2.1 % did not reply. A knowledge test revealed the significant frequency of misconception, with nearly half of the respondents (46.3 %) assuming that illness might be contracted by eating or coming into touch with wild animals. Wearing a facial mask is highly practiced (M = 3.59, SD = 0.91), followed by avoiding crowded places (M = 3.44, SD = 0.95) and practicing hand hygiene (M = 3.36, SD = 1.04). Females, the elderly, and the less educated, on the other hand, have less understanding of COVID-19, making them especially susceptible to the pandemic. It is proposed that further awareness might contribute to a favorable attitude and practice.

Aim: To characterize and analyze polymorphism of the MPT64 gene and evaluate AgMPT64-based immunochromatographic assay (ICA) specificity associated with polymorphism. Materials & methods: A total of 1449 suspected samples were tested for tuberculosis (TB), and the MPT64/ rv1980c gene was sequenced using next-generation sequencing for polymorphism analysis. Results: Of the TB-positive individuals, 200 (13.80%), 186 (12.84%) and 129 (8.90%) were positive using the liquid culture, GeneXpert and fluorescence microscopy assays, respectively. Liquid culture medium-based samples were confirmed using ICA, in which 193 (96.5%) were positive while seven (3.5%) were negative. Out of 14 sequenced samples, seven were positive and seven negative; 13 were identical to the reference and just one (ICA positive) showed a C477A point mutation (F159L). Conclusion: The results indicate that AgMPT64 can be considered as a potent vaccine candidate.

This research study focused on the economic impact of covid-19 on small and medium entrepreneurs. This research study was conducted in seven districts of Khyber Pakhtunkhwa. A total of 350 samples were randomly selected from seven districts. From each district 50 samples were selected including 25 small and 25 medium entrepreneurs. All the samples were taken from auto, hoteling, grocery, fresh food and garments industries. The results showed that stay-at-home policy inflicted huge economic cost both on small and medium entrepreneurs in Khyber Pakhtunkhwa. On average a small entrepreneur in Khyber Pakhtunkhwa lost US $1552.8 per day while every medium entrepreneur lost US $13084.2 per day in the garments industry during covid-19 lock down. Similarly, per day average cost of a small entrepreneur in Khyber Pakhtunkhwa was US $898.7 while that of the medium entrepreneur was US $6140.65 during covid-19 lock down. This financial lost/cost did not include any past or current liabilities rather it was derived from the sale and purchase data collected from the local entrepreneurs in Khyber Pakhtunkhwa.

The recent COVID-19 pandemic has brought attention to the strategies of quarantine and other governmental measures, such as lockdown, media coverage on social isolation, strengthening of public safety, etc. All these strategies are because to manage the disease as there is no vaccine and appropriate medicine for treatment. The mathematical model can assist to determine whether these intervention options are the most effective ones for illness control and how they might impact the dynamics of the disease. Motivated by this, in this manuscript, a classical order nonlinear mathematical model has been proposed to analyze the pandemic COVID-19. The model has been analyzed numerically. The suggested mathematical model is classified into susceptible, exposed, recovered, and infected classes. The non-standard finite difference scheme (NSFDS) is used to achieve the approximate results for each compartment. The graphical presentations for various compartments of the systems that correspond to some real facts are given via MATLAB.

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. Keywords: Breast cancer; TP53; CDH1; ATM; Risk Allele; Genotype.

COVID-19 disease caused by the SARS-CoV-2 virus has shaken our health and wealth foundations. Although COVID-19 vaccines will become available allowing for attenuation of disease progression rates, distribution of vaccines can create other challenges and delays. Hence repurposed drugs against SARS-CoV-2 can be an attractive parallel strategy that can be integrated into routine clinical practice even in poorly-resourced countries. The present study was designed using knowledge of viral pathogenesis and pharmacodynamics of broad-spectrum antiviral agents (BSAAs). We carried out the virtual screening of BSAAs against the SARS-CoV-2 spike glycoprotein, RNA dependent RNA polymerase (RdRp), the main protease (Mpro) and the helicase enzyme of SARS-CoV-2. Imatinib (a tyrosine kinase inhibitor), Suramin (an anti-parasitic), Glycyrrhizin (an anti-inflammatory) and Bromocriptine (a dopamine agonist) showed higher binding affinity to multiple targets. Further through molecular dynamics simulation, critical conformational changes in the target protein molecules were revealed upon drug binding which illustrates the favorable binding conformations of antiviral drugs against SARS-CoV-2 target proteins. The resulting drugs from the present study in combination and in cocktails from the arsenal of existing drugs could reduce the translational distance and could offer substantial clinical benefit to decrease the burden of COVID-19 illness. This also creates a roadmap for subsequent viral diseases that emerge. Communicated by Ramaswamy H. Sarma

The publication of the first draft of human genome, has led to the explosion of high throughput technologies including genomics, epigenomics, transcriptomic, proteomics, and metabolomics aiming to characterize the various biological molecules (DNA, RNA, proteins, and metabolites). These high throughput technologies collectively called as omics revolutionized medical research in the last two decades. The advent of next generation sequencing (NGS) reduced the time and economic cost of traditional sequencing and has led to the emergence of genomics as the first discipline of omics. Following the emergence of genomics, a number of projects such as The Cancer Genome Atlas (TCGA), 1000 Genome Project (1KGP), and the International Cancer Genome Consortium have been accomplished. These projects contributed significantly to the understanding of genetic variations in different cancers, for instance, TCGA produced over 2.5 petabytes of big data. Furthermore, the big data produced by these mega projects has been made publicly available to the clinicians and researchers to fast-track the diagnosis and prognosis of complex rare diseases. In developed countries, a multi-omics approach has been applied holistically to the clinical practice for the diagnosis and prognosis of various cancers and rare Mendelian diseases.

Non-synonymous missense SNPs (nsSNPs) in CPE and GNAS genes were investigated computationally. In silico identified nsSNPs were experimentally validated in type II diabetes mellitus (T2DM) in Pakistani Pathan population using next generation sequencing (NGS). Sixty two high-risk nsSNPs in CPE and 44 in GNAS were identified. Only 12 in GNAS were clinically significant. Thirty six high-risk nsSNPs in CPE and 08 clinically significant nsSNPs in GNAS lies in the most conserved regions. I-mutant predicted that nsSNPs decrease the proteins stability and ModPred predicted 20 and 12 post-translational modification sites in CPE and GNAS proteins respectively. Ramachandran plot showed 88.7% residues are in the most favored region of protein models. By experimentation, none of the nsSNPs were found to be associated with T2DM. In conclusion, this study differentiates the deleterious nsSNPs from the neutral ones. Although nsSNPs are not associated with T2DM, they can be targeted in other CPE and GNAS genes related disorders.

More than 200 countries across the globe, including Pakistan, have closed educational institutions (schools, colleges, universities and madrassas) to contain the spread of coronavirus (COVID-19 pan...

In this paper, the depositional environment, age, and tectonic context of the Sub-Himalayan Kuldana Formation are discussed in detail. To determine the Kuldana Formation’s depositional environment, age, and tectonic setting, sedimentological, palaeontological, and petrographic investigations have been conducted accordingly. The Kuldana Formation lithologically consists of both siliciclastic and carbonate rocks. Petrographically, the Kuldana Formation’s sandstone is divided into litharenite and feldspathic litharenite petrofacies. The sandstone plots on the QtFL and QmFLt suggest that the sandstone of the Kuldana Formation derived from a recycled orogen provenance field that developed during the collision of the Indian and Eurasian plates in the Lesser and Higher Himalayas. The plots in the diamond diagram further demonstrate that the detritus of the Kuldana Formation was derived from low and middle-to-upper rank metamorphic rocks of the Himalayas. Throughout the deposition of sandstone, paleo-climate conditions were semi-humid to semiarid. Dolostone and limestone are the two main types of carbonate rocks found in the Kuldana Formation. According to Dunham’s Classification, the Kuldana Formation limestone is classified as mudstone, wackstone, and packstone. These petrofacies suggest that the limestone was deposited in an inner-outer ramp setting. The bioclasts include bivalves, brachiopods, crinoid, gastropods, Globigerinoides spp., Lockhartia pustulosa, miliolids, Nummulites atacicus, Nummulites discorbina, Nummulites mamillatus, Nummulites djodjokartae, Nummulites vascus, and ostracods suggesting that the age of Kuldana Formation is Middle Eocene-early Oligocene. The Kuldana Formation was deposited during the initial stages of the Himalayan Orogeny as a result of the Ceno-Tethys Ocean’s regression and transgression, as revealed by a succession of siliciclastic and non-clastic rocks.

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.

This study focuses on suicidal ideation in victims of sexual abuse. Drawing upon semi-structured interviews of thirty victims of sexual abuse in Khyber Pukhtunkhwah, Pakistan, this paper discusses the theme, i.e. domestic violence, including indiscriminate sexual abuse and the abhorring crime of incest, which remains hidden due to aggressively upheld patriarchal norms of women exploitation. The interviews conducted at six different locations, present women's narratives of their untold plight for the first time. The findings of this research show that among the respondents, only those women had strong suicidal ideations who were the victims of incest. Irritation, aggression and self-deprecating behaviour were strong symptoms of their suicidal temptations. Pain, physical and emotional, caused by overwhelming stress in the form of familial and social hatred, social disconnectedness, burdensomeness and the previous history of violence were the main factors that highly escalated their risk factor in committing suicide

Chronic Myeloid Leukaemia (CML) is characterized by BCR-ABL1 mutation. A number of research studies have published reports of concomitant JAK2-V617F mutation in BCR-ABL positive Chronic Myeloid Leukaemia. This study aims to investigate the frequency of JAK2-V617F mutation in BCR-ABL positive CML cases. After approval from ethical committee, participants were enrolled in the study. A total of 103 samples from CML patients were analysed for the presence of JAK2-V617F mutation using real-time polymerase chain reaction. Patients were monitored for treatment response using real-time quantitative PCR for BCR-ABL1 mutation. Out of 103 samples analysed, 2 patients tested positive for JAK2-V617F mutation. These two patients when treated with standard Tyrosine Kinase Inhibitors (TKI) therapy achieved molecular response and normalized the haemoglobin and white cell counts. However, one patient has sustained thrombocytosis. JAK2 remained positive throughout the treatment course. We could not follow the second patient till the end of the study. JAK2 mutation in BCR-ABL1 mutated CML appears to be rare. Treatment with TKI does not appear to reduce JAK2 mutation burden despite a decrease in BCR-ABL1 copy numbers.

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. Supplementary Information The online version contains supplementary material available at 10.1007/s00284-021-02743-y.

OBJECTIVE: To find out the self-motivated cadence of intestinal microbiota by zinc obtainability with help of next generation sequencing. METHODS: This cross-sectional study was conducted on infants aging 1-4 months from Peshawar, Pakistan. Out of 50 infants enrolled in study, data of 46 healthy infants [23 breast-fed (BF) and 23 formula-fed (FF)] were available for final analysis. Their blood and stool samples were collected and analyzed for zinc and fecal DNA extraction, for metagenomic shot gun sequencing using next generation. RESULTS: Mean age of infants was 78.40±35.88 days. Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria are the four dominating major phyla found in the gut microbiota of the sample population. In breast-fed infants, mean plasma zinc was 0.138 ± 0.118 mg/L whereas, in formula-fed infants it was 0.120±0. 026 mg/L. Correlation of zinc levels with gut microbes revealed that Phylum Bacteroidetes was very low in breast-fed while in formula-fed infants it was negligible to an extent that cannot be correlated with zinc. It was also observed that there is abundance of Proteobacteria (BF: r=-0.276, p=0.264) and (FF: r= -0.043, p= 0.873) in both the zinc deficient groups whereas, Firmicutes content was (BF: r= 0.392, p=0.207) and (FF: r= -0.030, p= 0.905). CONCLUSION: Both breast-fed and formula-fed infants had low gut microbial diversity due to low zinc levels emphasizing the need to address and rectify this problem. The improved zinc status of the infants will enable the researchers to establish and ascertain the association of zinc status with the diversity of microbiome.

In this paper, we aimed to characterize the fecal microbiome and its resistomes of healthy and diseased subjects infected with multidrug-resistant Escherichia coli using next-generation sequencing (NGS). After initial screening, 26 stools samples belonging to healthy (n = 13) and diseased subjects (n = 13) were selected and subjected to NGS. A total of 23 and 42 antibiotic-resistant genes (ARGs) conferring resistance to 6 and 9 classes of antibiotics were identified in the resistomes of healthy and diseased subjects, respectively. Bacteroidetes were found to be the major phylum in both healthy and diseased subjects, however, Proteobacteria was predominantly present in the diseased subjects only. Microbial dysbiosis and predominance of various ARGs in the resistome of diseased subjects reflect the excessive usage of antibiotics in Pakistan and warrants immediate attention to regulate the use of various antimicrobials.

The study was designed to investigate the fecal microbiome and resistome of broiler chickens infected with multidrug-resistant (MDR) Escherichia coli (E. coli). Fecal samples (n = 410) from broiler chickens were collected from thirteen randomly selected sites of Khyber Pakhtunkhwa and screened for the presence of MDR E. coli. Upon initial screening, thirteen (13) MDR E. coli isolates were then subjected to shotgun metagenome next-generation sequencing (NGS). NGS based resistome analysis identified the multidrug efflux pump system-related genes at the highest prevalence (36%) followed by aminoglycoside (26.1%), tetracycline (15.9%), macrolide-lincosamide-streptogramin (9.6%), beta-lactam (6.6%), rifampin (2%), sulphonamide (1.3%), phenicol (0.91%), vancomycin (0.62%), trimethoprim (0.34%), colistin (0.30%), and quinolone (0.33%). The most abundant virulence-associated genes (VAGs) identified were iroN, iutA, iss, and iucA. NGS based taxonomic profiling at the phylum level revealed the predominance of Proteobacteria (38.9%) followed by Firmicutes (36.4%), Bacteroidetes (15.8%), and Tenericutes (8.9%). Furthermore, pathobionts such as E. coli, Salmonella enterica, Klebsiella pneumoniae, and Shigella flexneri belonging to the family Enterobacteriaceae were predominantly found. This study revealed the widespread presence of MDR genes, diverse VAGs, and a dysbiotic gut in the broiler chickens infected with MDR E. coli of Khyber Pakhtunkhwa for the first time using NGS.

The rapid breakout of the coronavirus disease of 2019 (COVID-19) has been declared pandemic with serious global concern due to high morbidity and mortality. As we enter the phase beyond limitations there is an urgent need for explicit treatment against COVID-19. To face this immediate global challenge, drug development from scratch is a lengthy process and unrealistic to conquer this battle. Drug repurposing is an emerging and practical approach where existing drugs, safe for humans, are redeployed to fight this harder to treat disease. A number of multi clinical studies have repurposed combined cocktail (remdesivir + chloroquine and favipiravir + chloroquine) to be effective against COVID-19. However, the exact mechanistic aspect has not yet been revealed. In the present study, we have tried to decipher the mechanistic aspects of existing medicines at the viral entry and replication stage via the structural viroinformatics approach. Here we implied the molecular docking and dynamic simulations with emphasis on the unique structural properties of host receptor angiotensin-converting enzyme 2 (ACE2), SARS-CoV2 spike protein and RNA dependent RNA polymerase enzyme (RdRp) of the SARS-CoV2. Deep structural analysis of target molecules exposed key binding residues and structural twists involved in binding with important pharmacophore features of existing drugs [(7-chloro-N-[5-(diethylamino)pentan-2-yl]quinolin-4-amine (chloroquine),N-[[4-(4-methylpiperazin-1-yl)phenyl]methyl]-1,2-oxazole-5-carboxamide N-[[4-(4-methylpiperazin-1-yl)phenyl]methyl]-1,2-oxazole-5-carboxamide) (SSAA09E2), 2-ethylbutyl (2S)-2-{[(S)-{[(2R,3S,4R,5R)-5-{4-aminopyrrolo[2,1-f][1,2,4]triazin-7-yl}-5-cyano-3 (remdesivir) and 6-Fluor-3-oxo-3,4-dihydro-2-pyrazincarboxamid (favipiravir)]. It is evident from this structural informatics study that combo of chloroquine + SSAA09E2 with remdesivir or favipiravir could significantly restrain the virus at the entry and replication stage. Thus, drug repurposition is an attractive approach with reduced time and cost to treat COVID-19, we don't have enough time as the whole world is lockdown and we are in urgent need of an obvious therapeutics' measures.

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.

BackgroundThe ongoing COVID-19 pandemic caused by SARs-CoV-2 was transmitted person to person via droplet infections and fecal-oral transmission. This illustrates the probability of environmentally facilitated transmission, mainly the sewage.MethodWe 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.ResultsA 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 patients and COVID 19 patient quarantine center drainage 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.DiscussionThis study finding indicates that SARs-CoV-2 detection through wastewater surveillance has an epidemiologic potential that can be used as early warning system to monitor viral tracking and circulation in cities with lower COVID-19 disease burden or heavily populated areas where door-to-door tracing may not be possible. However, attention 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.

Aim: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a pernicious viral disease, causes acute respiratory distress responsible for mortality and morbidity worldwide. To screen different immunomodulatory medicinal compounds to unravel their interaction with SARS-CoV-2 viral proteins. Materials & methods: A library of immunomodulatory medicinal compounds with antiviral capability were analyzed against SARS proteases, spike protein and nonstructural proteins (NSP-9, 15) using Autodock vina. Results: Out of more than 300 medicinal compounds, only six compounds: arzanol, ferulic acid, genistein, resveratrol, rosmanol and thymohydroquinone showed significant interaction with the SARS viral proteins by forming hydrogen bonds with the active site residues with low binding energy. Further ADMET (absorption, distribution, metabolism, excretion and toxicity) analysis showed good pharmacokinetic properties and low acute toxicity of these compounds. Conclusion: The current study provides convincing evidence that these medicinal compounds exert antiviral activity against the SARS-CoV-2 virus and could be further exploited for the treatment of this disease.

Background: Microbiota plays an important role in food safety and its alteration poses a serious threat to humans. Comparative microbiome profiling using next-generation sequencing (NGS) enabled the understanding of microbial diversity and similarity between different species. In this study, we used NGS to profile the fecal microbiota of sick human and broiler chickens. A total of 26 fecal samples were collected from severely sick human subjects (n= 13) and broiler chickens (n=13) with similar symptoms. Results: The total number of microbial species detected in broiler chickens fecal microbiota was higher than that of humans. Phylum Proteobacteria was the most abundant in both human and broiler chickens fecal microbiota while Tenericutes was found to be least abundant in both species. Phylum Actinobacteria was found only in the human fecal microbiota. In both humans and broiler chickens, E.coli was found to be phylogenetically related suggesting a microbial association between both species. Conclusion: NGS based taxonomic profiling revealed the association of microbial dysbiosis with extreme sickness in both humans and broiler chickens. The dominance of phylum Proteobacteria in both the species ascertains their altered gut microbiota. Both human and broiler chickens microbial communities were found to be genetically related indicating horizontal transfer of microbes between the two species.

Soil organic carbon (SOC) sequestration is one of the major agronomic measures to mitigate green house gas emission, enhance food security, and improve agriculture sustainability. The study, theref...

Soon after its emergence in Wuhan, China in late December, the novel coronavirus (SARS-CoV-2) spread rapidly to the other parts of the world and acquired a pandemic status. Pakistan reported its first case of SARS-CoV-2 on February 26, 2020, in Karachi. Since then, a higher prevalence of COVID-19 was reported from almost all major cities of Pakistan. Owing to the high rate of COVID-19, Pakistan enforced a lockdown across the whole country on March 24, 2020. This lockdown controlled the SARS-CoV-2 successfully; however, severe economic losses were observed in the lockdown Standard Operating Procedure (SOP) guidelines. We, therefore, proposed an alternative plan termed as “regulated reverse lockdown” which will help decrease the burden of COVID-19 without having a negative effect on the economy. The present editorial will address the potential flaws in the already imposed lockdown and will propose an alternative plan to make the lockdown more effective in terms of COVID-19 prevalence and economic growth of Pakistan.

Objective: In Pakistan, 74% of consanguineous marriages are among the first cousins. Continuity of consanguineous marriages over generations increases the risk of recessive diseases such as deafness. The objective of this study was to investigate genetic origin of Pakistani deaf brothers with parents of consanguineous marriage. Methods: DNA was extracted from the blood through Qiagen kit. Paired-end sequencing library was prepared according to protocol of Illumina’s TruSight Rapid Capture kit and TruSight Inherited Disease Panel. Library was normalized and used for Next Generation Sequencing through MiSeq. NGS data were analyzed using various bioinformatics tools. Results: Both brothers were found to have novel deleterious mutation in MYO7A (c.2476G>A) while the younger brother had additional novel deleterious mutation in TH (c.43C>T) and EVC2 (c.2614C>T) genes. Conclusion: It is concluded that in addition to novel mutations in MYO7A, TH and EVC2, the CDH23 and GJB2 can also be responsible for deafness in the family with consanguineous marriages. How to cite this:Sabiha B, Ali J, Yousafzai YM, Haider SA. Novel deleterious mutation in MYO7A, TH and EVC2 in two Pakistani brothers with familial deafness. Pak J Med Sci. 2019;35(1):17-22. doi: https://doi.org/10.12669/pjms.35.1.98 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

The occurrence of microbial communities harboring antibiotic resistance bacteria and antibiotic resistance genes in the drinking water distribution system pose a significant threat to the aquatic ecosystem and to public health, especially in developing countries. In this study, we have used next-generation sequencing technology to explore bacterial community diversity and the abundance of antibiotic resistance genes in biofilms collected from the drinking water distribution system of Peshawar, the capital city of the Khyber Pakhtunkhwa province of Pakistan. The results showed that Proteobacteria were the most abundant phyla (89.79%) in all biofilm samples, followed by Bacteroidetes (3.48%) and Actinobacteria (2.79%). At genus level, Pseudomonas was the most common (22.45%) in all biofilm samples. Overall, bacterial diversity and richness was higher in biofilm samples collected from the consumer end than the source site. Bacterial diversity was also dependent on the piping material (GI vs. PVC) and water supply (direct vs. indirect). Functional annotation reveals a differential abundance of common metabolic pathways at source and consumer end. Resistome analysis revealed a prevalence of resistance genes against 12 classes of antibiotics in all samples with macrolides resistance being the commonest at the consumer end (42.1%) and fluoroquinolone resistance at the source end (24%). To our knowledge, this is the first study that provides new insight and evidence into the microbial community diversity and antibiotic resistance in the drinking water supply system of Peshawar. These findings may ultimately help the authorities to design and implement effective strategies for controlling biofilms and ensuring a continuous supply of safe drinking water to the community.

Objectives: To assess the role of double J stent in management of renal andureteric calculi measuring 1.5 to 2.5 cm size prior to ESWL. Period: 1st January 2015 to 30thDecember 2015. Study Design: Retrospective study. Methods: We included 120 patientswhich were divided in two groups. In group A we took 40 patients in whom double J stentswere inserted before ESWL while in group B, 80 patients underwent ESWL without stenting. Weincluded patients of both sex having radio-opaque stones in kidney or proximal ureter measuring1.5cm to 2.5cm in size in adults (age > 18) years where stone fragmentation resulted afterESWL. The average stone size in both groups was comparable (p > 0.05). Patients with urinarytract infections, pregnancy, radiolucent stones, bleeding disorders, larger or small stones,anatomical abnormality, nonfunctioning kidney and where ESWL was not successful after thirdsession were excluded from study. The patients were randomized on basis of their choice foreither procedure and majority 80 patients (66 %) refused stenting before ESWL due to fearof invasive procedure and socioeconomic reasons. Patient’s pre-operative investigations likecomplete blood count, urea/creatinine, X-ray & ultrasound KUB and IVU were done. ESWL wasdone without anesthesia and after complete clearance of fragments stents were removed withinthree months. Results: Out of 120 patients 70 were male (58.33 %) and 50 were female (41.66%). In group A (with ureteric stenting) there was no ureteric obstruction noticed after ESWLand fragments clearance resulted with mild pain or discomfort in 12(10%) patients. There wasdelayed clearance of the fragments in patients but that had no impact on patient daily activities.While in group B (without ureteric stenting) 30 (37.5%) patients developed complications likesevere colicky pain for which they were hospitalized whereas remaining 50(62.5%) patientshad mild to moderate pain with stein-stresse appearance which was managed using oral andsystemic analgesics, increase oral fluids and reassurance to the patients. The time of stonefragments clearance was delayed in group A as compared to group B (p < 0.05). Conclusion:We conclude that double J stent should be passed prior to ESWL in cases of large renal andureteric calculi to avoid severe colicky pain.

Objective To investigate the prevalence of Staphylococcus aureus ( S. aureus ) isolated from skin wards of the hospitals of Khyber Pakhtunkhwa, its resistance against various commonly and commercially available antibiotics, as well as different genetic traits of resistance and their correlations with the phenotypic visible resistance. Methods In the present study a simple PCR technique were used to investigate the genetic traits of resistance in S. aureus isolated from skin wards of two major hospitals of Khyber Pakhtunkhwa, Pakistan. A total of 100 samples were collected from both the male and female, of which 50 were from patient's site of infection and 50 from ward environment. Results These results demonstrated that the total prevalence of S. aureus both in ward as well as in patients was 48%. The S. aureus prevalence was the highest in female patients (50%) followed by ward environment (29%) and then male patients (21%). The antibiotic sensitivity tests revealed that the highest (91.6% isolates) sensitivity was shown to imipenem. However, the highest resistance was found to be against penicillin (100% isolates) followed by cefotaxime (75% isolates). In addition, only 29% of the isolates were found to be resistant to methicillin. PCR technique based on the previously designed primers targeting different genetic traits of resistance revealed that 13 out of the 14 isolates resistant to methicillin were positive for mecA gene. blaZ Genetic traits were found in all isolates resistant to penicillin. The multi-drug resistance traits, vgaA and vgaB each was detected only in 12.5% of S. aureus isolates. The phenotypic character of antibiotic resistance is highly correlated to different genetic traits of resistance. Conclusions Based on our findings, it is concluded that antibiotic resistance in S. aureus strains is increasing day by day due to self-medications and medication by non-registered medical practitioners. Therefore, for quick and fast detection, we propose next-generation sequencing be utilized to screen for antibiotic resistance.

The role of different growth media and chemical enhancer on synthesis of secondary metabolites Cladosporium resinae (NRL-6437) was investigated for their in vitro biological activities. Cladosporium resinae (NRL-6437) were grown in various nutrient media (Czapeak-dox Broth (CB), Czapeak Yeast-extract Broth (CYB), Yeast Extract Sucrose (YES), Potato Dextrose Broth (PDB) and Czapeak-dox (supplemented with glucose and starch) Broth (CGSB) for the production of metabolites. Two chemical epigenetic modifiers (suberoyl-anilide hydroxamic acid (SAHA) and 5-azacytidine (5-AZA) were also used for the expression of silent genes for secondary metabolite production. Our results indicated that among different media, Czapeak yeast extract broth produced more secondary metabolites. Application of 15mM of both modifiers was effective for the expressions of silent genes resulting in an increased metabolites production. Secondary metabolites extracted in ethyl acetate and fractionized in n-Hexane were also tested for their biological activity. The secondary metabolites revealed varying degrees of growth inhibitions of the tested organisms. Similarly, these metabolites were also active against brine shrimps and Lemna.