Dataset Information

Cross Sectional Study and Risk Factors Analysis of Francisella tularensis in Soil Samples in Punjab Province of Pakistan.

ABSTRACT: Tularemia is an endemic zoonotic disease in many parts of the world including Asia. A cross-sectional study was conducted to determine genome-based prevalence of Francisella tularensis (Ft) in soil, assess an association between its occurrence in soil and likely predictors i.e., macro and micro-nutrients and several categorical variables, and determine seroconversion in small and large ruminants. The study included a total of 2,280 soil samples representing 456 villages in eight districts of the Punjab Province of Pakistan followed by an analysis of serum antibodies in 707 ruminants. The genome of Ft was detected in 3.25% (n = 74, 95% CI: 2.60-4.06) of soil samples. Soluble salts (OR: 1.276, 95% CI: 1.043-1.562, p = 0.015), Ni (OR: 2.910, 95%CI: 0.795-10.644, p = 0.106), Mn (OR:0.733, 95% CI:0.565-0.951, p = 0.019), Zn (OR: 4.922, 95% CI:0.929-26.064, p = 0.061) and nutrients clustered together as PC-1 (OR: 4.76, 95% CI: 2.37-9.54, p = 0.000) and PC-3 (OR: 0.357, 95% CI: 0.640, p = 0.001) were found to have a positive association for the presence of Ft in soil. The odds of occurrence of Ft DNA in soil were higher at locations close to a water source, including canals, streams or drains, [?2 = 6.7, OR = 1.19, 95% CI:1.05-3.09, p = 0.004] as well as places where animals were present [?2 = 4.09, OR = 2.06, 95% CI: 1.05-4.05, p = 0.02]. The seroconversion was detected in 6.22% (n = 44, 95% CI: 4.67-8.25) of domestic animals. An occurrence of Ft over a wide geographical region indicates its expansion to enzootic range, and demonstrates the need for further investigation among potential disease reservoirs and at-risk populations, such as farmers and veterinarians.

SUBMITTER: Muhammad J

PROVIDER: S-EPMC6460113 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Cross Sectional Study and Risk Factors Analysis of Francisella tularensis in Soil Samples in Punjab Province of Pakistan.

Muhammad Javed J Rabbani Masood M Shabbir Muhammad Zubair MZ Muhammad Khushi K Ghori Muhammad Taslim MT Chaudhry Haroon Rashid HR Ul Hassnain Zia Z Jamil Tariq T Abbas Tariq T Chaudhry Muhammad Hamid MH Haisem-Ur-Rasool Muhammad M Ali Muhammad Asad MA Nisar Muhammad M Kirimanjeswara Girish S GS Jayarao Bhushan M BM

Frontiers in cellular and infection microbiology 20190405

Tularemia is an endemic zoonotic disease in many parts of the world including Asia. A cross-sectional study was conducted to determine genome-based prevalence of Francisella tularensis (Ft) in soil, assess an association between its occurrence in soil and likely predictors i.e., macro and micro-nutrients and several categorical variables, and determine seroconversion in small and large ruminants. The study included a total of 2,280 soil samples representing 456 villages in eight di ...[more]

PMID: 31024860

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Project description:Francisella tularensis, the bacterium that causes the zoonosis tularemia, and its genetic near neighbor species, can be difficult or impossible to cultivate from complex samples. Thus, there is a lack of genomic information for these species that has, among other things, limited the development of robust detection assays for F. tularensis that are both specific and sensitive. The objective of this study was to develop and validate approaches to capture, enrich, sequence, and analyze Francisella DNA present in DNA extracts generated from complex samples. RNA capture probes were designed based upon the known pan genome of F. tularensis and other diverse species in the family Francisellaceae. Probes that targeted genomic regions also present in non-Francisellaceae species were excluded, and probes specific to particular Francisella species or phylogenetic clades were identified. The capture-enrichment system was then applied to diverse, complex DNA extracts containing low-level Francisella DNA, including human clinical tularemia samples, environmental samples (i.e., animal tissue and air filters), and whole ticks/tick cell lines, which was followed by sequencing of the enriched samples. Analysis of the resulting data facilitated rigorous and unambiguous confirmation of the detection of F. tularensis or other Francisella species in complex samples, identification of mixtures of different Francisella species in the same sample, analysis of gene content (e.g., known virulence and antimicrobial resistance loci), and high-resolution whole genome-based genotyping. The benefits of this capture-enrichment system include: even very low target DNA can be amplified; it is culture-independent, reducing exposure for research and/or clinical personnel and allowing genomic information to be obtained from samples that do not yield isolates; and the resulting comprehensive data not only provide robust means to confirm the presence of a target species in a sample, but also can provide data useful for source attribution, which is important from a genomic epidemiology perspective.

Project description:BACKGROUND:Malaria is the fifth leading cause of death worldwide. Pakistan is considered as a moderate malaria-endemic country but still, 177 million individuals are at risk of malaria. Roughly 60% of Pakistan's population, live in malaria-endemic regions. The present study is based upon the survey of various health care centers in 10 major cities of Northern and Southern Punjab to find out the malarial infection patterns in 2015. The diagnosis, seasonal variations, age and gender-wise distribution of Plasmodium spp. circulating in the study area were also included in the objectives. METHODS:The malaria-suspected patients '16075' were enrolled for malaria diagnosis using microscopy, out of which 925 were malaria positive which were processed for molecular analysis using nested PCR. The 18S rRNA genes of Plasmodium species were amplified, sequenced, blast and the phylogenetic tree was constructed based on sequences using online integrated tool MEGA7. RESULTS:The 364 cases recruited from Northern Punjab with the highest incidence in Rawalpindi (25.5%) and lowest in Chakwal (15.9%). From Southern Punjab 561 cases were enlisted Rajanpur (21.4%) maximum and lowest from Multan and Rahim Yar Khan (18%). The slide positivity rate, annual parasite incidence, and annual blood examination rates were 5.7 per 1000 population, 0.1, and 0.2% respectively. The only P. vivax (66.7%), P. falciparum (23.7%) and mixed infection by these two species (9.6%) were diagnosed. The same trend (P. vivax?>?P. falciparum?>?mixed infection) in species identification %age was confirmed from molecular analysis. However, the occurrence of malaria was higher in Southern Punjab (5.5%) as compared to the Northern Punjab (4.0%). The overall malaria percentage occurrence of treatment-seeking patients in all recruited cities of Punjab was 4.9%. The age-group of 1-20 and males among genders were more affected by malaria. The comparison of different seasons showed that the malaria infection was at a peak in Summer and post-monsoon. CONCLUSION:The incidence of malaria was high in the flood infected rural areas of Southern Punjab, Summer, and post-monsoon. The age group (1-20) and gender-wise males were more affected by malaria.

Project description:BackgroundBecause of diverse topographical habitats, the Chenab River wetland harbors a wealth of medicinal and food plant species. This paper presents first quantitative assessment on the ethnobotanical use of plants by the local peoples residing in the Chenab riverine area.MethodsThe ethnobotanical data were collected from six parts of the Chenab River wetland: Mandi Bahuddin, Gujranwala, Gujrat, Sargodha, and Sialkot during 2014 to 2015, using semi-structured interviews. Quantitative indices including informant consensus factor (FCI), relative frequency of citation (RFC), relative importance level (RIL), use value (UV), fidelity level (FL), and corrected fidelity level (CFL) were used to analyze the data.ResultsOn the whole, 129 medicinal plant species belonging to 112 genera of 59 families were reported, with herbs as dominant life forms (51%). Poaceae was the leading family with 13 species, and leaves were the most frequently utilized plant parts (28%). Herbal medicines were mostly used in the form of powder or decoction, and were mainly taken orally. Withania somnifera, Solanum surattense, Solanum nigrum, Azadirachta indica, Ficus benghalensis, Morus nigra, Morus alba, Polygonum plebeium, and Tribulus terrestris were among the highly utilized plant species, with highest UV, RFC, RIL, FL, and CFL values. The reported ailments were grouped into 11 categories based on FCI values, whereas highest FIC was recorded for gastrointestinal diseases and glandular diseases (0.41 and 0.34, respectively). The use report (UR) and frequency of citation (FC) depicted strong positive correlation (r = 0.973; p = 0.01). The value of determination (r2 = 0.95) indicating 95% variation in UR can be explained in terms of the FC.ConclusionThe significant traditional knowledge possessed by local communities depicts their strong relation with phytodiversity. Reported data could be helpful in sustainable use and protection of plant species in the Chenab wetland, with special emphasis on medicinal plants. Furthermore, screening of plant-borne active ingredients and in vivo/in vitro pharmacological activities could be of interest for novel drug synthesis.

Project description:ObjectivesPrime focus of this study was to evaluate the availability and affordability of originator brands (OBs) and lowest price generics (LPGs) of prescribed biologic and non-biologic anticancer medicines.Design, settings and participantsA descriptive, cross-sectional survey was conducted in 22 cancer-care hospitals (18 public hospitals and 4 private hospitals) and 44 private pharmacies in Punjab, Pakistan. Sampling population consisted of 4483 patients with cancer aged ?18 years. The availability was determined by classifying anticancer medicines in four categories: absent/unavailability (medicines not present in any surveyed facility), low availability (medicines present in <50% of surveyed facilities), fairly high availability (medicines present in 50%-74% of surveyed facilities) and high availability (medicines present in >75% of surveyed facilities). Medicines were affordable if overall cost of all the prescribed anticancer medicines were 20% of the household capacity to pay. Data were analysed by using Statistical Packages for Social Sciences (IBM SPSS Statistics for Windows, V.21.0).ResultsA total of 5060 patients with cancer were approached out of which 4483 patients were included in the survey. Overall, 10?103 anticancer drugs were prescribed. Among them, 96.3% were non-biologics and 3.7% were biologics. Oncologists were reluctant to prescribe biologics due to high prices. 58.1% of non-biologics were affordable; whereas, the affordability of biologics was 3.3%. A total of 43.9% of both biologic and non-biologic OBs were available; whereas, their affordability was 44.2%. On the other hand, the availability of LPGs was 21.3%, and their affordability was 66.1%. For low-income patients, the affordability of non-biologics was 31.6% and the affordability of biologics was 1.1%.ConclusionsMost of the patients with cancer were prescribed non-biologics due to their low price and better affordability. In contrast to OBs, LPGs of both biologics and non-biologics had less availability but more affordability.

Project description:BackgroundTo investigate the antimicrobial (AM) use and prescribing patterns at primary health care centers (PHCCs) in Punjab, Pakistan.MethodsA cross-sectional study was designed according to the World Health Organization (WHO) methodology for AM usage from January, 2017 to June, 2017. Standard data collection forms designed by the WHO were used to collect the data from 32 PHCCs (16 rural healthcare centers (RHCs) and 16 basic health units (BHUs)) in Punjab province of Pakistan. PHCCs were randomly selected from 8 main cities. The study sample consisted of prescription records of 6400 outpatients (200 prescriptions records from each PHCC) and 800 inpatients (25 inpatient records from each PHCC). Data of the year 2016 were collected retrospectively by using systematic random sampling technique and analyzed through SPSS.ResultsAmong the hospital indicators, standard treatment guidelines (STGs) regarding the infectious diseases were not available in PHCCs. Number of days during which key AMs were out of stock was 12.1 days per month (range = 3.1-19.2). Out of total PHCC medicines costs, expenditures on AMs were 26.2% (range = 17.1-39.0). In case of prescribing indicators, the average number of AMs per prescription was 1.4 (range = 1.1-1.7), percentage of prescriptions prescribed with AMs was 81.5% (range = 68.9-89.1) and duration of AM treatment on average was 5.1 days per patient (range = 3.3-6.4). Average cost of prescribed AMs per patient was 1.3 USD (range = 0.6-4.3). The PHCCs prescribed a median of 5 (range = 3-9) types of AMs, including 10 (range = 5-15) individual agents. Out of 79.3% prescriptions of outpatients prescribed with AMs, only 16.4% were properly prescribed. Out of 100% prescriptions of inpatients prescribed with AMs, 12.1% were properly prescribed. Out of all the AM prescriptions 23.6% contained penicillins, 20.1% contained cephalosporins and 19.4% contained fluoroquinolones Metronidazole (18.0%), ciprofloxacin (16.5%) and co-amoxiclav (14.3%) were most commonly prescribed AMs.ConclusionsIn PHCCs, AMs were prescribed more frequently. However large proportions of these prescriptions were inappropriate. Continuous education and training of medical staff and cost effective policies could play an important role in promotion of rational use of AMs.

Dataset Information

Cross Sectional Study and Risk Factors Analysis of Francisella tularensis in Soil Samples in Punjab Province of Pakistan.

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Cross Sectional Study and Risk Factors Analysis of <i>Francisella tularensis</i> in Soil Samples in Punjab Province of Pakistan.

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