Whole-Genome Sequencing of a Mycobacterium tuberculosis Strain Belonging to Lineage 1 (Indo-Oceanic) and the East African Indian Spoligotype, Isolated in Jazan, Saudi Arabia.
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ABSTRACT:
SUBMITTER: Abdelhaleem A
PROVIDER: S-EPMC7427191 | biostudies-literature | 2020 Aug
REPOSITORIES: biostudies-literature
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Whole-Genome Sequencing of a Mycobacterium tuberculosis Strain Belonging to Lineage 1 (Indo-Oceanic) and the East African Indian Spoligotype, Isolated in Jazan, Saudi Arabia.
Abdelhaleem Aymen A Hershan Almonther A Agarwal Pradeep P Farasani Abdullah A Omar Shaheed V SV Ismail Arshad A Allam Mushal M
Microbiology resource announcements 20200813 33
We describe here the draft genome sequence of AY1MRC, a <i>Mycobacterium tuberculosis</i> strain belonging to lineage 1 (Indo-Oceanic) and the East African Indian spoligotype, isolated from a patient with tuberculosis in Jazan, Saudi Arabia. ...[more]
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Project description:The East African-Indian (EAI) family of Mycobacterium tuberculosis is an endemic group mainly observed in Southeast Asia. Here, we report the complete genome sequence of an M. tuberculosis strain isolated as a member of the EAI family in Hanoi, Vietnam, a country with a high incidence of tuberculosis.
| S-EPMC5473266 | biostudies-literature
Project description:For a long time, the people of Saudi Arabia have been using medicinal plants (MPs) as conventional medicine to heal diverse human and livestock diseases. The present work is the first study on ethnobotanical uses of 124 MPs species used by the local tribal communities of Jazan province in the Southwest of Saudi Arabia. Ethnobotanical data were collected by interviewing 174 local informants using semistructured interviews. Informants of different ages, from several settlements belonging to several tribal communities, were interviewed. It is worth noticing that the age of informants and their knowledge of MPs were positively correlated, whereas the educational level and MP knowledge of participants were negatively correlated. To find out if there was agreement in the use of certain plants in the treatment of given ailments, we used Informant Consensus Factor (ICF). To determine the most frequently used plant species for treating a particular ailment category by local people we used the fidelity level (FL%). The Relative Frequency of Citation (RFC) was used to indicate the local importance of a species and the relative importance (RI) level was used to check the therapeutic potentials of the cited plants. A total of 124 MPs belonging to 103 genera and 48 families were collected and identified. The majority of these plants were shrubs (45%), perennial herbs (21%), annual herbs (19%), or trees (18%). The Asteraceae (10.48%), Fabaceae (7.25%), and Apocynaceae (7.25%) families were the most represented. Leaves, fruits, and whole plant (24%, 18%, and 16%, respectively) were the most used plant parts in formulating traditional medicines. Ziziphus spina-christi and Calotropis procera with the highest RI level (2.0) were found to have the highest range of therapeutic uses. They were followed by Datura stramonium (1.86), Withania somnifera, and Aloe vera (1.81). The ICF ranged from 0.02 to 0.42 covering 12 disease categories with a prevalence of disease categories related to skin and hair problems (ICF=0.42) having 75 species cited, while 73 species were cited for gastrointestinal tract (GIT) disorders (ICF = 0.40). Senna alexandrina (67%), Tribulus terrestris (64%), Pulicaria undulata (60%), Leptadenia pyrotechnica (55%), and Rumex nervosus (55%) had the highest FL which indicates their good healing potential against specific diseases. The high-FL species are the most promising candidate plants for in-depth pharmacological screening and merit further consideration. Accordingly, Jazan flora has good ethnobotanical potential. Unfortunately, many MP species are endangered by drought, overgrazing, and overexploitation. Some protection measures should be undertaken to prevent these species from becoming extinct. Natural reserves and wild nurseries are typical settings to retain medically important plants in their natural habitats, while botanic gardens and seed banks are important paradigms for ex situ conservation.
| S-EPMC6582903 | biostudies-literature
Project description:Avoidance of medication errors is imperative for the safe use of medications, and community pharmacists are uniquely placed to identify and resolve the errors that may arise due to poorly handwritten prescriptions. Purpose: To explore the opinion and attitudes of community pharmacists towards poor prescription writing and their suggestions to overcome this concern. Methods: A cross-sectional, self-administered survey was conducted among the community pharmacists in the Jazan region, Saudi Arabia. Descriptive analysis and chi-square test were used at 5% p-value (p > 0.05) as the significance level. Results: The response rate for the survey was 78.66%, and 140 community pharmacists agreed to participate. Among the study subjects, the majority (73.57%) had a bachelor's degree. Nearly three-fourths (3/4) of the pharmacists (72.29%) chose to send the patient back to the prescriber when they found difficulty in interpreting the information from an illegible prescription. As many as 80.71% of the pharmacists believed that poorly handwritten prescriptions were the cause of actual errors when dispensing medications. The most commonly encountered problem due to poorly handwritten prescriptions was the commercial name of medicine, which was reported by around two-thirds (67.86%) of the pharmacists. The use of e-prescription was suggested by 72.86% of the pharmacists as a probable solution to encounter this problem. Conclusion: Our findings highlight the belief and attitudes of community pharmacists in the region and their opinions to solve this impending problem of poor prescription writing. Continuous professional development courses can be adopted to tackle the problem. Additionally, health authorities can work on incorporating and facilitating the use of e-prescription in the community sector, which can be a boon to physicians, pharmacists, and patients. Proper and extensive training is however needed before the implementation of e-prescribing.
| S-EPMC8391709 | biostudies-literature
Project description:The aim of this study was to measure anxiety levels and many co-factors that might influence the levels of anxiety during the COVID-19 outbreak in southern Saudi Arabia (KSA). A cross-sectional self-reporting survey was conducted to determine the level of generalized anxiety disorder (GAD) symptoms related to COVID-19 and quarantining. We selected a convenience sample of eligible participants who had been invited online through social media apps. The survey instrument was distributed, and 981 participants responded. Of the total sample, almost 90% were under the age of 40, 75% were women, and 77% had an educational level beyond high school. Just over half were single, with nearly all participants Saudi nationals. The overall prevalence of anxiety related to COVID-19 was 27%. Factors most strongly related to reporting anxiety included having a diagnosis of COVID-19, spending 1- ≥ 3 h focused on COVID-19, having a previous mental illness history, being a current or former smoker, being female, having a previous diagnosis of chronic or respiratory illness, being below age 40, having a limited standard of living, and being a student. Our study reveals how critical it is to emphasize preventive mental health care during pandemics and what factors may make some individuals most vulnerable to anxiety. Further research is recommended to examine GAD levels pre, during and post pandemic. Additional research to explore the long-term impact of the pandemic on mental health is also needed. being a student, and a limited standard of living.
| S-EPMC9106396 | biostudies-literature
Project description:COVID-19 vaccine acceptance and refusal vary across countries and among different socio-demographic groups. This study investigates hesitancy related to the COVID-19 vaccine and the associated factors in the rural-community-dominated Jazan Province, Saudi Arabia. A cross-sectional study through an online questionnaire was conducted from February to April 2021 to investigate the extent of vaccine hesitancy related to the COVID-19 vaccine and the associated factors in the Jazan region. A Chi-squared test and post hoc analysis were conducted to analyze the statistical significance of the association between variables. Of the 569 participants who completed the online questionnaire, the majority were males (81.5%) and had a university education (72.6%). Of the participants, more than one-third (36.9%) were hesitant to vaccinate. Concern about adverse side effects following vaccination was the most reported reason for vaccine hesitancy (42.6%), followed by beliefs that the vaccine was unsafe or ineffective (15.5%). The data analysis revealed that people who lived in cities in Jazan Province or those who did not have a family history of COVID-19 infection were more likely to be vaccine hesitant. It is more important than ever to develop and implement community-based strategies to address vaccine hesitancy, especially in rural areas.
| S-EPMC10706323 | biostudies-literature
Project description:BackgroundArtemisinin-based combination therapy (ACT) is recommended at the initial phase for treatment of Plasmodium falciparum, to reduce morbidity and mortality in all countries where malaria is endemic. Polymorphism in portions of P. falciparum gene encoding kelch (K13)-propeller domains is associated with delayed parasite clearance after ACT. Of about 124 different non-synonymous mutations, 46 have been identified in Southeast Asia (SEA), 62 in sub-Saharan Africa (SSA) and 16 in both the regions. This is the first study designed to analyse the prevalence of polymorphism in the P. falciparum k13-propeller domain in the Jazan region of southwest Saudi Arabia, where malaria is endemic.MethodsOne-hundred and forty P. falciparum samples were collected from Jazan region of southwest Saudi Arabia at three different times: 20 samples in 2011, 40 samples in 2016 and 80 samples in 2020 after the implementation of ACT. Plasmodium falciparum kelch13 (k13) gene DNA was extracted, amplified, sequenced, and analysed using a basic local alignment search tool (BLAST).ResultsThis study obtained 51 non-synonymous (NS) mutations in three time groups, divided as follows: 6 single nucleotide polymorphisms (SNPs) '11.8%' in samples collected in 2011 only, 3 (5.9%) in 2011and 2016, 5 (9.8%) in 2011 and 2020, 5 (9.8%) in 2016 only, 8 (15.7%) in 2016 and 2020, 14 (27.5%) in 2020 and 10 (19.6%) in all the groups. The BLAST revealed that the 2011 isolates were genetically closer to African isolates (53.3%) than Asian ones (46.7%). Interestingly, this proportion changed completely in 2020, to become closer to Asian isolates (81.6%) than to African ones (18.4%).ConclusionsDespite the diversity of the identified mutations in the k13-propeller gene, these data did not report widespread artemisinin-resistant polymorphisms in the Jazan region where these samples were collected. Such a process would be expected to increase frequencies of mutations associated with the resistance of ACT.
| S-EPMC7653757 | biostudies-literature
Project description:The conventional morphological characterization of mosquito species remains heavily used for species identification in Jazan, Saudi Arabia. It requires substantial expertise and time, as well as having difficulty in confirming identity of morphologically similar species. Therefore, to establish a reliable and accurate identification system that can be applied to understanding spatial distribution of local mosquito species from the Jazan region, DNA barcoding was explored as an integrated tool for mosquito species identification. In this study, 44 adult mosquito specimens were analyzed, which contain 16 species belong to three genera of potential mosquito disease vectors (Aedes, Anopheles, and Culex). The specimens were collected from the Jazan region located in southwest Saudi Arabia. These included old and preserved mosquito voucher specimens. In addition, we assessed the genetic distance based on the generated mitochondrial partial COI DNA barcodes to detect cryptic diversity across these taxa. Nine mosquito species belonging to three genera were successfully barcoded and submitted to GenBank, namely: Aedes aegypti, Aedes caspius, Aedes vexans, Aedes vittatus, Anopheles arabiensis, Culex pipiens, Culex quinquefasciatus, Culex sitiens, and Culex tritaeniorhynchus. Of these nine species, Aedes vexans, Aedes vittatus, Culex sitiens, and Culex tritaeniorhynchus were registered in GenBank for the first time from Saudi Arabia. The DNA barcodes generated a 100% match to known barcodes of these mosquito species, that also matched with the morphological identification. Ae. vexans was found to be either a case of cryptic species (subspecies) or a new species from the region. However, more research has to be conducted to prove the latter. This study directly contributes to the development of a molecular reference library of mosquito species from the Jazan region and Saudi Arabia. The library is essential for confirmation of species in support of existing mosquito surveillance and control programmes.
| S-EPMC9171578 | biostudies-literature
Project description:Determination of human immunodeficiency virus-1 (HIV-1) genotypes and identification of antiretroviral drug-resistant mutations. Among treatment naïve HIV patients in Jazan, Saudi Arabia. HIV is a major public health problem. HIV genotyping and antiretroviral resistance testing is an important guide for better management of treatment-naive. Antiretroviral resistance testing before starting of treatment regimen leads to a better virological response. A total of 57 samples of treatment-naive patients were collected from King Fahd Central Hospital in Jazan, Saudi Arabia. Samples were tested for HIV-1 antibodies, western blot, viral load, HIV-1 genotypes through direct sequencing, and antiretroviral resistance testing. The HIV-1 Genotypes were as follow; C: 66.6%, D: 10.5%, G: 8.8%, B: 7.0%, CRF01_AE: 3.5%, A and CRF02_AG: 1.8% each. 77.2% of cases showed susceptibility to the 3 major classes of antiretroviral drugs; Protease inhibitor (PI), Nucleoside reverse transcriptase inhibitor (NRTI), and non-nucleoside reverse transcriptase inhibitors (NNRTI); while 8.8% had mutations conferring resistance to NRTI. Mutations conferring resistance to PI were detected in 7.0% of cases, and 1.8% of cases had mutations conferring resistance to both NRTI and PI. Mutations conferring resistance to NNRTI were detected in 5.3% of cases. Mutations associated with antiretroviral drugs include (V82A+I84IV), (L10F+Q58E), (L10F+V82Y), L10FV, L33LF, L89LMV, M184V, E138A, V106I, and V179VD. The prevalence of HIV-1 antiretroviral resistance mutations is 22.8% in the studied population, which may warrant antiretroviral drug resistance testing as a pretreatment to help and guide physicians for the proper HIV treatment.
| S-EPMC7717766 | biostudies-literature
Project description:BackgroundBurnout is a syndrome that results from stressors in the work environment that have not been successfully managed. The prevalence of burnout among schoolteachers was always controversial. COVID-19 pandemic added more stressors to teachers since they had to change their working styles in response to the pandemic lockdowns or curfews. In Saudi Arabia, the prevalence and determinants of burnout among school teachers were not measured by any other group during the COVID-19 pandemic stressors.MethodsA cross-sectional survey was conducted among 879 teachers in the Jazan region, Saudi Arabia, using the Maslach Burnout Inventory (MBI), during April 2021. Multistage cluster random sampling was used.ResultsThe mean age of the participants was 41.4 (±6.9) years. Male teachers represented 52.6% of the participants while females represented 47.4%. Most teachers showed burnout symptoms (69.6%). Consequences of burnout were observed, such as using psychotropic medications (4.6%), absenteeism (45.6%), lack of job satisfaction (7.7%), and changing schools (15.8%). Using the MBI scale, most teachers showed medium or high emotional exhaustion (57.6%), low depersonalization (62.2%), and low personal accomplishment (51.4%).ConclusionMost teachers showed symptoms of burnout during the COVID-19 pandemic. Being an expert and ability to adapt to technology during the COVID-19 pandemic proved to effectively reduce burnout symptoms. Increasing incentives, early detection, and improving the work environment is recommended to diminish burnout consequences.
| S-EPMC9205293 | biostudies-literature
Project description:BackgroundFirst aid during a seizure is critical, but many people in Jazan, Saudi Arabia may not know what to do. This is because epilepsy is often stigmatized in the region and regarded as a spiritual or mental disorder. This study investigated the awareness of seizure first aid among the population living in Jazan.MethodsAn online survey was conducted. Healthcare workers and people who had never heard of epilepsy were excluded. Participants were asked to identify correct measures of seizure first aid from a list of 20 statements [9 correct and 11 incorrect]. A composite awareness score was calculated by subtracting the number of incorrect statements from the number of correct statements. Participants were classified into three groups: high, intermediate, and low awareness. Logistic regression was used to identify factors associated with high awareness.ResultsOf the 1215 participants, 80.5 % had low awareness of seizure first aid. The most common correct responses were clearing the area of dangerous objects (91.3 %), putting a pillow under the neck (69.3 %), and timing the seizure (68.5 %). However, only 32.2 % knew to tell the person what happened after the seizure. The most common misconception was that an ambulance should be called immediately, regardless of the details (88.3 %). Other common misconceptions included putting something in the person's mouth (87.5 %), holding them down (83.0 %), taking out their contact lenses (79.9 %), and giving antiseizure medications orally (73.2 %). People who previously watched an educational video on seizure first aid (OR = 4.27, 95 % CI = 1.48-12.34, p = .007) or who knew someone with epilepsy (OR = 9.01, 95 % CI = 2.82-28.83, p < .001) were more likely to have a high awareness of seizure first aid.ConclusionThe study found that most people in Jazan, Saudi Arabia do not know how to provide first aid for seizures. The findings inform future research and highlight the need for increased education and training on seizure first aid in this region.
| S-EPMC10692802 | biostudies-literature