We present a genome assembly from an individual female Entiminae weevil, Polydrusus pterygomalis (Arthropoda; Insecta; Coleoptera; Curculionidae). The genome sequence has a total length of 1,051.50 megabases. Most of the assembly is scaffolded into 11 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 20.95 kilobases in length.
Background: Burkholderia thailandensis is an environmental bacteria closely related to Burkholderia pseudomallei that rarely causes infection in humans. Some environmental isolates have shown to express a capsular polysaccharide known as B. thailandensis capsular variant (BTCV), but human infection has not previously been reported. Although B. thailandednisis has been identified in environmental samples in Laos before, there have not been any human cases reported.
Case: A 44-year-old man presented to a district hospital in Laos with a short history of fever and pain in his left foot. Physical examination identified a deep soft-tissue abscess in his left foot and an elevated white blood count. A deep pus sample was taken and melioidosis was suspected from preliminary laboratory tests. The patient was initially started on cloxacillin, ceftriaxone and metronidazole, and was then changed to ceftazidime treatment following local melioidosis treatment guidelines.
Laboratory methods: A deep pus sample was sent to Mahosot Hospital microbiology laboratory where a mixed infection was identified including Burkholderia sp. Conventional identification tests and API 20NE were inconclusive, and the B. pseudomallei-specific latex agglutination was positive. The isolate then underwent a Burkholderia species specific PCR which identified the isolate as B. thailandensis. The isolate was sent for sequencing on the Illumina NovaSeq 6000 system and multi-locus sequence typing analysis identified the isolate had the same sequence type (ST696) as B. thailandensis E555, a strain which expresses a B. pseudomallei-like capsular polysaccharide.
Conclusion: This is the first report of human infection with B. thailandensis in Laos, and the first report of any human infection with the B. thailandensis capsular variant. Due to the potential for laboratory tests to incorrectly identify this bacteria, staff in endemic areas for B. thailandensis and B. pseudomallei should be aware and ensure that appropriate confirmatory methods are used to differentiate between the species.
Background: The focus on P. falciparum diagnosis has led to an underestimation of the global burden of malaria resulting from neglected Plasmodium species. However, there is still scarce data on the prevalence of P. ovale species (spp) globally. To address this knowledge gap, data collected from cross-sectional studies in Kilifi county were used to: 1) determine the prevalence of P. ovale spp infections; and 2) determine the sensitivity of different diagnostic assays in detecting P. ovale spp infections.
Methods: A total of 531 individuals were sampled across three study sites in Kilifi County, Kenya between 2009 and 2020. Blood smears were prepared from peripheral blood and screened for Plasmodium parasite stages using light microscopy. Molecular screening involved DNA extraction of dried blood spots and blood in ethylenediaminetetraacetic acid, polymerase chain reaction (PCR) using primers targeting the 18 small ribosomal subunit and sequencing.
Results: Microscopy screening revealed that the most prevalent species was P. falciparum (32.0%) followed by P. malariae (9.0%) and then P. ovale spp( 1.5%). PCR screening identified additional P. ovale spp positives cases. Overall PCR results indicate that43 (8.1%) out of the 531 individuals harbored P. ovale spp infection with the highest prevalence reported in the tertiary health facility, (14.6%, 95% CI 8-23.6%), followed by the primary health facility (8.3%, 95% CI 5.4-11.9%), and the community from a cross-sectional blood survey, (3.6%, 95% CI 1.2-8.2%). Microscopy screening for P. ovale spp had a low sensitivity of 7% (95% CI 1-19-30%) and a high specificity of 99% (95% CI 98-100%). Sequencing results confirmed the presence of P.ovale curtisi.
Conclusions: This study provides baseline data for P.ovale spp surveillance in Kilifi County, primarily using PCR to improve diagnosis. These results suggest that malaria elimination and eradication efforts should not only concentrate on P. falciparum but should embrace a holistic approach towards elimination of all Plasmodium spp.
Background: Hypertension affects over one billion people worldwide, posing a significant global health burden. Clinical practice guidelines could play a key role in guiding healthcare providers in improving hypertension management. However, how the quality of hypertension CPGs differs across country income settings is not well understood. This study aims to explore variation in the quality of hypertension CPGs, comparing low-, middle-, and high-income countries, using the Appraisal of Guidelines for Research and Evaluation (AGREE) II tool.
Methods: A Medline and grey literature search was conducted to identify hypertension CPGs in English from every country from January 2012 to September 2022. Two reviewers independently assessed and scored each CPG against the AGREE II tool. Results were described and the Kruskal-Wallis test was used to test for statistically significant difference in the domain scores across country income groups.
Results: Forty-three CPGs were included for analysis from across income settings. Guidelines from HICs scored higher in four out of the six domains. The highest scoring domain was 4: "clarity and presentation" (median score 83%), the lowest scoring was domain 6 "editorial independence" (median score 0%). Statistically significant differences between income settings were observed for domain 3 "rigour of development" (p <0.001), domain 4 "clarity and presentation" (p = 0.03) and domain 6 "editorial independence" (p = 0.04).
Conclusions: Whilst some variation exists in guideline quality across country income levels, the greatest degree of variation exists across the domains of the AGREE II tool. Global efforts to improve the quality of hypertension guidelines should focus on the transparent statement of editorial independence of guideline committees and apply rigorous replicable methods in the authoring of guidelines. Establishing national and international communities of practice to collaborate across income settings may reduce duplication of resource, allow for shared learning and promote the development of high-quality hypertension CPGs.
Foreign body (FB) aspiration is a life-threatening medical emergency that usually presents with a history of choking episodes, followed by cough and shortness of breath. However, when the signs and symptoms are subtle, they can be easily missed by the parents or the child, causing delays in the diagnosis and management, suspecting other respiratory illnesses. Here, we report an eight years old neurologically stable girl without a history of choking episodes, with only subtle respiratory symptoms, with a candy wrapper stuck in the left bronchus missed by X-ray and computer tomography (CT)- scan of the chest and diagnosed and removed by flexible bronchoscopy.
Background: Data reusability is the driving force of the research data life cycle. However, implementing strategies to generate reusable data from the data creation to the sharing stages is still a significant challenge. Even when datasets supporting a study are publicly shared, the outputs are often incomplete and/or not reusable. The FAIR (Findable, Accessible, Interoperable, Reusable) principles were published as a general guidance to promote data reusability in research, but the practical implementation of FAIR principles in research groups is still falling behind. In biology, the lack of standard practices for a large diversity of data types, data storage and preservation issues, and the lack of familiarity among researchers are some of the main impeding factors to achieve FAIR data. Past literature describes biological curation from the perspective of data resources that aggregate data, often from publications.
Methods: Our team works alongside data-generating, experimental researchers so our perspective aligns with publication authors rather than aggregators. We detail the processes for organizing datasets for publication, showcasing practical examples from data curation to data sharing. We also recommend strategies, tools and web resources to maximize data reusability, while maintaining research productivity.
Conclusion: We propose a simple approach to address research data management challenges for experimentalists, designed to promote FAIR data sharing. This strategy not only simplifies data management, but also enhances data visibility, recognition and impact, ultimately benefiting the entire scientific community.
Background: To study pain, data on pain characteristics, possible triggers and consequences - such as the impact of pain on people's lives - need to be available. When not collated, described and/or organised in a systematic manner, it can be difficult to assess how useful an existing dataset may be for one's project. This data note describes and categorises the complex and multi-modal indices of pain available in the Avon Longitudinal Study of Parents and Children (ALSPAC).
Methods: Data from two generations of the ALSPAC cohort; index child participants (Generation 1, G1), their mothers and fathers/mothers' partners (Generation 0, G0) were used. Search terms such as 'pain', 'ache', 'hurt', 'sore', specific pain conditions, labour pain and methods of pain relief were used to identify pain and pain-related variables. These data were extracted from all waves of data collection. We developed pain categories and subsequently categorised variables in an iterative process. Repeated measurements of the same variables over waves of data collection were also identified.
Results: We identified 21 categories of pain variables, which were subsequently grouped into themes: pain characteristics, extended pain characteristics and causes, treatment for pain, pain interference and pain-related to specific events. Pain and pain-related data have been collected from G1 participants, G0 mothers, and G0 partners, although there are fewer data for the partners. There were some repeated measurements, most commonly, of pain location. As is typical with longitudinal birth cohort studies, maternal proxy-reports were used during participants' younger years and self-reports were utilised from adolescence onwards.
Conclusions: Researchers interested in studying pain can feasibly do so in two generations of a regional UK population who have been followed up over 30 years. ALSPAC can be used to study pain from the early years through to young adulthood and in mothers from the perinatal period onwards.
Background: Scrub typhus is a neglected life-threatening vector-borne disease mainly caused by the bacterium Orientia tsutsugamushi, which is occasionally transmitted to humans during feeding of larval mites. It has been estimated that more than 1 billion persons are potentially threatened and 1 million clinical cases occur annually across the world; however, it is unclear how this estimate was computed (and what the original source was) and much remains unknown regarding its global burden and risk factors. This systematic review aims to provide a comprehensive overview of the spatial-temporal distribution of scrub typhus, associated burden and risk factors at global, national and subnational resolutions, and to review the burden estimation models used at those different scales.
Methods: A systematic search for literature on scrub typhus occurrence, risk factors and modelling methods will be conducted. PubMed and five other databases will be searched for published literature, and Google Scholar and nine other databases will be used to search for grey literatures. All titles/abstracts of the searched records will be separately assessed by two reviewers, who will then screen the full-text of potential records to decide eligibility. A pre-formatted spreadsheet will be used by one reviewer to extract data from qualifying research, with a second reviewer checking the results. Data will be tabulated, synthesized descriptively, and summarized narratively for each review question. Where appropriate, meta-analyses will be conducted. The risk of bias will be assessed, and potential publication bias will be detected.
Discussion: This review will provide a comprehensive understanding of the current occurrence, spatial-temporal distribution, and burden of scrub typhus, identify associated risk factors from global to subnational resolutions, consolidate the best practice modeling framework(s) to estimate the burden of scrub typhus at various geographic/temporal resolutions, and decompose the relative contributions of various risk factors at scale.
Prospero registration: CRD42022315209.
We present a genome assembly from an individual female Molossus alvarezi (Chordata; Mammalia; Chiroptera; Molossidae). The genome sequence is 2.490 Gb in span. The majority of the assembly is scaffolded into 24 chromosomal pseudomolecules, with the X sex chromosomes assembled.
Background: Antimicrobial use in Laos is among the highest in Southeast Asia. The first Lao comprehensive antimicrobial prescribing guidelines have been available since 2021. This study explored the determinants of antibiotic prescribing decisions and how the new prescribing guidelines were being used.
Methods: In August 2022, in-depth interviews were conducted with 16 Lao prescribers from two hospitals. Participants were questioned about their prescribing behaviours, attitudes to guidelines, how they learned about the guidelines and factors influencing their uptake. The interviews were audio-recorded, transcribed, and translated into English. Thematic analysis of the transcripts was conducted.
Results: Lao prescribers considered multiple factors before deciding to prescribe antibiotics to their patients. The most common factor was based on the clinical judgement of the prescribers. Lack of certain antibiotics and turnaround times of laboratory results were the main challenges to prescribing antibiotics appropriately. The majority of participants were satisfied with the guidelines, regarding them as comprehensive, simple and convenient. However, most participants admitted that they did not access the guidelines very often. The main reason was that they could remember the treatment recommendations because they treat similar diseases on a daily basis. Improving antibiotic knowledge was the most common recommendation in order to improve the appropriate use of antibiotics. Raising awareness of the guidelines and promoting their use should also be considered. In addition, heads of the wards, and policy and implementation leaders, should support, monitor and feedback their use to encourage all prescribers to follow the guidelines.
Conclusions: Several factors contribute to enhancing appropriate antibiotic prescription. Key factors for improving antibiotic prescription include enhancing prescribers' clinical knowledge, ensuring access to essential antibiotics, and updating guidelines regularly. Health leaders must get involved to promote their use.
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