bluuebunny/crossref_metadata_2025_split huggingface dataset:
rRNA operon improves species-level classification of bacteria and microbial community analysis compared to 16S rRNA
Authors: Won Sohyoung , Cho Seoae , Kim Heebal 
Published: October 2024

ABSTRACT

Precise identification of species is fundamental in microbial genomics and is crucial for understanding the microbial communities. While the 16S rRNA gene, particularly its V3-V4 regions, has been extensively employed for microbial identification, however has limitations in achieving species-level resolution. Advancements in long-read sequencing technologies have highlighted the rRNA operon as a more accurate marker for microbial classification and analysis than the 16S rRNA gene. This study aims to compare the accuracy of species classification and microbial community analysis using the rRNA operon versus the 16S rRNA gene. We evaluated the species classification accuracy of the rRNA operon,16S rRNA gene, and 16S rRNA V3-V4 regions using a BLAST-based method and a k-mer matching-based method with public data available from NCBI. We further performed simulations to model microbial community analysis. We accessed the performance using each marker in community composition estimation and differential abundance analysis. Our findings demonstrate that the rRNA operon offers an advantage over the 16S rRNA gene and its V3-V4 regions for species-level classification within the genus. When applied to microbial community analysis, the rRNA operon enables a more accurate determination of composition. Using the rRNA operon yielded more reliable results in differential abundance analysis as well.

IMPORTANCE
We quantitatively demonstrated that the rRNA operon outperformed the 16S rRNA and its V3-V4 regions in accuracy for both individual species identification and species-level microbial community analysis. Our findings can provide guidelines for selecting appropriate markers in the field of microbial research.
Dietary amino acids, macronutrients, vaginal birth, and breastfeeding are associated with the vaginal microbiome in early pregnancy
Authors: Corbett Gillian A. , Moore Rebecca , Feehily Conor , Killeen Sarah Louise , O'Brien Eileen , Van Sinderen Douwe , Matthews Elizabeth , O'Flaherty Roisin , Rudd Pauline M. , Saldova Radka , Walsh Calum J. , Lawton Elaine M. , MacIntyre David A. , Corcoran Siobhan , Cotter Paul D. , McAuliffe Fionnuala M. 
Published: October 2024

ABSTRACT

The vaginal microbiome is a key player in the etiology of spontaneous preterm birth. This study aimed to illustrate maternal environmental factors associated with vaginal microbiota composition and function in pregnancy. Women in healthy pregnancy had vaginal microbial sampling from the posterior vaginal fornix performed at 16 weeks gestation. After shotgun metagenomic sequencing, heatmaps of relative abundance data were generated. Community state type (CST) was assigned, and alpha diversity was calculated. Demography, obstetric history, well-being, exercise, and diet using food frequency questionnaires were collected and compared against microbial parameters. A total of 119 pregnant participants had vaginal metagenomic sequencing performed. Factors with strongest association with beta diversity were dietary lysine (adj-
R
2
0.113,
P
= 0.002), valine (adj-
R
2
0.096,
P
= 0.004), leucine (adj-
R
2
0.086,
P
= 0.003), and phenylalanine (adj-
R
2
0.085,
P
= 0.005, Fig. 2D). Previous vaginal delivery and breastfeeding were associated with vaginal beta diversity (adj-
R
2
0.048,
P
= 0.003; adj-
R
2
0.045,
P
= 0.004), accounting for 8.5% of taxonomy variation on redundancy analysis. Dietary fat, starch, and maltose were positively correlated with alpha diversity (fat +0.002 SD/g,
P
= 0.025; starch +0.002 SD/g,
P
= 0.043; maltose +0.440 SD/g,
P
= 0.013), particularly in secretor-positive women. Functional signature was associated with CST, maternal smoking, and dietary phenylalanine, accounting for 8.9%–11% of the variation in vaginal microbiome functional signature. Dietary amino acids, previous vaginal delivery, and breastfeeding history were associated with vaginal beta diversity. Functional signature of the vaginal microbiome differed with community state type, smoking, dietary phenylalanine, and vitamin K. Increased alpha diversity correlated with dietary fat and starch. These data provide a novel snapshot into the associations between maternal environment, nutrition, and the vaginal microbiome.

IMPORTANCE
This secondary analysis of the MicrobeMom randomized controlled trial reveals that dietary amino acids, macronutrients, previous vaginal birth, and breastfeeding have the strongest associations with vaginal taxonomy in early pregnancy. Function of the vaginal niche is associated mainly by species composition, but smoking, vitamin K, and phenylalanine also play a role. These associations provide an intriguing and novel insight into the association between host factors and diet on the vaginal microbiome in pregnancy and highlight the need for further investigation into the complex interactions between the diet, human gut, and vaginal microbiome.
Epidemiology of pediatric meningitis and encephalitis in Japan: a cross-sectional study
Authors: Mizuno Shinsuke , Kusama Yoshiki , Otake Shogo , Ito Yusuke , Nozaki Masatoshi , Kasai Masashi 
Published: October 2024

ABSTRACT

Information on the epidemiology and cause-specific clinical features of pediatric meningitis and encephalitis is limited, owing to conventional laboratory methods' limitations in identifying causative pathogens. The FilmArray Meningitis/Encephalitis (FA-M/E) panel, a molecular diagnostic tool, can detect 14 pathogens within 1 hour. We investigated meningitis and encephalitis epidemiology among children in Japan and FA-M/E panels' utility in their clinical management. This cross-sectional study was conducted among children aged 0–18 years admitted to seven regional hospitals in western Japan between October 2022 and September 2023. Cerebrospinal fluid (CSF) samples were collected from 221 children and tested using the FA-M/E panel. Clinical and microbiological data were reviewed retrospectively. Fifty-eight patients tested positive using the FA-M/E panel. Viral and bacterial pathogens were detected in 49 and nine cases, respectively. Human parechovirus and enterovirus occurred mainly in epidemic clusters during the summer and were primarily detected in young infants. Patients who tested positive for human parechovirus had a significantly higher frequency of sepsis-like manifestations and a lower frequency of CSF pleocytosis than did those who tested positive for enterovirus. CSF pleocytosis was absent in 30 patients who tested positive using the FA-M/E panel. Among the patients who tested positive for bacteria, three of the nine were not diagnosed using conventional culture methods, owing to prior antimicrobial therapy. The FA-M/E panel can identify bacterial and viral pathogens causing pediatric meningitis and characterize the epidemiology in local communities.

IMPORTANCE
Culture and polymerase chain reactions have traditionally been used to identify microorganisms causing pediatric meningitis and encephalitis. However, the methods currently used to identify the causative microorganisms are limited, particularly in general hospitals. The FilmArray Meningitis/Encephalitis (FA-M/E) panel, a fully automated genetic testing system, can detect 14 pathogens using the multiplex polymerase chain reaction method. This study described the epidemiology of pediatric meningitis and encephalitis in Japan. The microorganisms causing acute meningitis and encephalitis in children in Japan were identified using the FilmArray Meningitis/Encephalitis panel. Testing cerebrospinal fluid using the FA-M/E panel is useful for the identification of the pathogen in children with community-acquired acute meningitis and encephalitis. This increases knowledge on the epidemiology and clinical manifestations of acute meningitis and encephalitis caused by specific pathogens and can be used to facilitate optimal patient management.
The microbiota of moon snail egg collars is shaped by host-specific factors
Authors: Piedl Karla , Aylward Frank O. , Mevers Emily 
Published: October 2024

ABSTRACT

Moon snails (Family: Naticidae) lay eggs using a mixture of mucus and sediment to form an egg mass commonly referred to as an egg collar. These egg collars do not appear to experience micro-biofouling or predation, and this observation led us to hypothesize that the egg collars possess a chemically rich microbiota that protect the egg collars from pathogens. Herein, we sought to gain an understanding of the bacterial composition of egg collars laid by a single species of moon snails,
Neverita delessertiana
, by amplifying and sequencing the 16S rRNA gene from the egg collar and sediment samples collected at four distinct geographical regions in southwest Florida. Relative abundance and non-metric multidimensional scaling plots revealed distinct differences in the bacterial composition between the egg collar and sediment samples. In addition, the egg collars had a lower α-diversity than the sediment, with specific genera being significantly enriched in the egg collars. Analysis of microorganisms consistent across two seasons suggests that
Flavobacteriaceae
make up a large portion of the core microbiota (36%–58% of 16S sequences). We also investigated the natural product potential of the egg collar microbiota by sequencing a core biosynthetic gene, the adenylation domains (ADs), within the gene clusters of non-ribosomal peptide synthetase (NRPS). AD sequences matched multiple modules within known NRPS gene clusters, suggesting that these compounds might be produced within the egg collar system. This study lays the foundation for future studies into the ecological role of the moon snail egg collar microbiota.

IMPORTANCE
Animals commonly partner with microorganisms to accomplish essential tasks, including chemically defending the animal host from predation and/or infections. Understanding animal–microbe partnerships and the molecules used by the microbe to defend the animals from pathogens or predation has the potential to lead to new pharmaceutical agents. However, very few of these systems have been investigated. A particularly interesting system is nutrient-rich marine egg collars, which often lack visible protections, and are hypothesized to harbor beneficial microbes that protect the eggs. In this study, we gained an understanding of the bacterial strains that form the core microbiota of moon snail egg collars and gained a preliminary understanding of their natural product potential. This work lays the foundation for future work to understand the ecological role of the core microbiota and to study the molecules involved in chemically defending the moon snail eggs.
Leveraging investments, promoting transparency and mobilising communities: a qualitative analysis of news articles about how the Ebola outbreak informed COVID-19 response in five African countries
Authors: Courtney Lauren P , Billaud Manon , Paulenich Alex , Chew Rob , Alidina Zainab , Pinto Meredith 
Published: October 2024

BackgroundThe WHO declared the novel COVID-19 outbreak a pandemic in March 2020. While the COVID-19 pandemic was unprecedented, prior experiences with diseases such as Middle East respiratory syndrome, severe acute respiratory syndrome and Ebola shaped many countries’ preparedness and response strategies. Although lessons learnt from outbreak responses have been documented from a variety of sources, news media play a special role through their dissemination of news to the general public. This study investigated news media to explore how lessons learnt from the West African Ebola outbreak in 2014–2016 informed the COVID-19 responses in several African countries.MethodsWe conducted qualitative analysis on a dataset of previously compiled COVID-19-related news articles published from 1 March 2020 to 31 August 2020. This dataset included 34,225 articles from 6 countries. We filtered the dataset to only include articles with the keyword ‘Ebola’. We used a machine-learning text classification model to identify relevant articles with clear and specific lessons learnt. We conducted inductive and deductive coding to categorise lessons learnt and identify emergent themes.ResultsOf the 861 articles containing the word ‘Ebola’, 18.4% (N=158) with lessons learnt from Ebola were included across five of the countries: Ethiopia, Ghana, Kenya, Liberia and Sierra Leone. News articles highlighted three emergent themes: the importance of leveraging existing resources and past response system investments, promoting transparency in public health messaging and engaging community leaders in all phases of the response.ConclusionsFindings suggest fostering trust prior to and throughout an outbreak facilitates timely implementation and compliance of mitigation strategies. Trust can be built by leveraging existing resources, being communicative and transparent about their funding allocation and decision-making and engaging communities.
The impact of a multi-faceted intervention on non-prescription dispensing of antibiotics by urban community pharmacies in Indonesia: a mixed methods evaluation
Authors: Ferdiana Astri , Mashuri Yusuf Ari , Wulandari Luh Putu Lila , Rahayu Ihsanti Dwi , Hasanah Miratul , Ayuningsih Zulfa , Batura Neha , Khan Mishal , Liverani Marco , Guy Rebecca , Schierhout Gill , Kaldor John , Law Matthew , Day Richard , Jan Stephen , Wibawa Tri , Probandari Ari , Yeung Shunmay , Wiseman Virginia 
Published: October 2024

IntroductionNon-prescription antibiotic dispensing is prevalent among community pharmacies in several low- and middle-income countries. We evaluated the impact of a multi-faceted intervention to address this challenge in urban community pharmacies in Indonesia.MethodsA pre-post quasi-experimental study was carried out in Semarang city from January to August 2022 to evaluate a 7-month long intervention comprising: (1) online educational sessions for pharmacists; (2) awareness campaign targeting customers; (3) peer visits; and (4) pharmacy branding and pharmacist certification. All community pharmacies were invited to take part with consenting pharmacies assigned to the participating group and all remaining pharmacies to the non-participating group. The primary outcome (rate of non-prescription antibiotic dispensing) was measured by standardised patients displaying symptoms of upper respiratory tract infection, urinary tract infection (UTI) and seeking care for diarrhoea in a child. χ2tests and multivariate random-effects logistic regression models were conducted. Thirty in-depth interviews were conducted with pharmacists, staff and owners as well as other relevant stakeholders to understand any persistent barriers to prescription-based dispensing of antibiotics.FindingsEighty pharmacies participated in the study. Postintervention, non-prescription antibiotics were dispensed in 133/240 (55.4%) consultations in the participating group compared with 469/570 (82.3%) in the non-participating group (p value <0.001). The pre-post difference in the non-prescription antibiotic dispensing rate in the participating group was 20.9% (76.3%–55.4%) compared with 2.3% (84.6%–82.3%) in the non-participating group (p value <0.001).Non-prescription antibiotics were less likely to be dispensed in the participating group (OR=0.19 (95% CI 0.09 to 0.43)) and more likely to be dispensed for the UTI scenario (OR=3.29 (95% CI 1.56 to 6.94)). Barriers to prescription-based antibiotic dispensing included fear of losing customers, customer demand, and no supervising pharmacist present.InterpretationMultifaceted interventions targeting community pharmacies can substantially reduce non-prescription antibiotic dispensing. Future studies to evaluate the implementation and sustainability of this intervention on a larger scale are needed.
Satisfaction survey on graduates of standardised training for resident doctors in Guizhou Province, China
Authors: Zhu Haijian , Zhang Chanchan , Li Na , Yang Zhe , Qian Xin , Ji Min , Yang Jing , Liu Mingkun , Yang Wei , Li Dongdong , Sun Jiangling 
Published: October 2024

ObjectivesThis study aimed to investigate the satisfaction levels of graduate residents in Guizhou Province and analyse the factors influencing their satisfaction.MethodsA cross-sectional survey was conducted using a simple random sampling method with all graduate residents from 24 hospitals in Guizhou Province. The survey covered the residents’ demographic information, information about the training hospitals and satisfaction survey responses. Statistical analyses were performed using SPSS 29.0, including descriptive statistics using component ratios, binomial distribution tests for specific satisfaction situations,X2tests for between-group comparisons and binary logistic regression analyses to analyse the associations between residency satisfaction and related factors. The significance level was set at α=0.05.ResultsThe survey included 1070 graduate residents of Guizhou Province, China, including 500 males (46.7%) and 570 females (53.3%). The satisfaction questionnaire revealed that 23.8% were very satisfied; 45.4% were somewhat satisfied; and 26.4%, 2.3% and 2.1% were average, somewhat dissatisfied and very dissatisfied, respectively. Factors influencing residency satisfaction included gender, age, training base level, identity type, training participation year and average monthly income.ConclusionBased on this study, the satisfaction of graduate residents in Guizhou Province, China, is relatively lower than that in other countries and provinces. Therefore, Guizhou Province should take appropriate measures to address these influencing factors and enhance residency training satisfaction, thereby improving the residency training quality.
Virtual simulation for teaching cardiology in nursing: a scoping review protocol
Authors: Carvalho Sabrina de Oliveira , Paz Ana Beatriz Barbosa , da Silva Machado Raylane , da Luz Phellype Kayyaã , Andrade Elaine Maria Leite Rangel , Luctkar-Flude Marian 
Published: October 2024

IntroductionVirtual simulation (VS) can be an effective learning strategy in the context of nursing education on cardiovascular disease; however, its use in teaching cardiology in nursing is less studied. The objective of this scoping review is to map the use of VS for teaching cardiology in nursing.Methods and analysisThis scoping review will be conducted according to the Joanna Briggs Institute methods, and the results will be reported according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews checklist. Eight databases will be searched: MEDLINE (NCBI/PubMed), Cumulative Index to Nursing and Allied Health Literature, Web of Science, Latin American and Caribbean Literature in Health Sciences, Spanish Bibliographic Index of Health Sciences, Database of Nursing, EMBASE and Google Scholar from inception to 31 July 2024. This study will include any existing peer-reviewed literature and grey literature. There will be no time or language restrictions. Two reviewers will screen and select the articles independently, and when there are differences, they will be resolved with a third opinion. When appropriate, broad themes and categories derived from the review questions will be accompanied by other illustrative formats (eg, tables or graphs, word clouds and infographics).Ethics and disseminationThis research project does not require ethical committee approval. The study is part of a cooperative research project between researchers from the Federal University of Piauí, Northeast of Brazil, and Queen’s University, Ontario, Canada, to develop and seek evidence of content validity of a VS game about valvular heart disease. The protocol and review will be published in peer-reviewed journals.Registration detailsOpen Science Framework (https://doi.org/10.17605/OSF.IO/S3UMH).
Effect of telemonitoring on the rate of dropout during home non-invasive ventilation: a retrospective study using a home care provider database
Authors: Le Mao Raphael , Gut Gobert Christophe , Texereau Joelle B , Kremer Frédérique , Goret Marion , Chekroun Martinot Aurélie , Rosé Mathieu , Trzepizur Wojciech , Gagnadoux Frédéric 
Published: October 2024

ObjectivesTelemonitoring (TM) of home non-invasive ventilation (NIV) has been shown to facilitate home/outpatient therapy set-up. However, the impact of long-term TM on therapy dropouts, compliance and leak control has not yet been clearly determined. This study evaluated whether the NIV dropout rate was reduced by TM combined with remote patient support compared with a non-telemonitoring (NTM) pathway.DesignRetrospective cohort study.SettingData were obtained from all agencies of a single home care provider in France.ParticipantsAdults with chronic respiratory failure (n=659) who started nocturnal NIV between January 2017 and December 2019 and had ≥8 days of NIV therapy (51% male; mean age 68.5±13.8 years; 35.5% on long-term oxygen therapy) were included. The TM group included 275 patients who spent ≥80% of the follow-up using TM, and the NTM group included 384 patients who had 0 to ≤10 days of telemonitoring during follow-up.Primary and secondary outcome measuresThe primary outcome was the rate of NIV dropouts at 1 year (ie, treatment discontinuation, excluding deaths). Secondary outcomes included therapy compliance and leaks.Results82 patients died during follow-up. Significantly fewer patients in the TM vs NTM group had dropped out of NIV therapy at 1 year (13% vs 34%; p<0.001). After adjustment for age, sex, NIV usage at 1-month follow-up and the main underlying respiratory disease, TM was significantly associated with a lower risk of dropout (HR 0.33, 95% CI 0.23 to 0.49; p<0.001). At 1, 4, 8 and 12 months, a greater proportion of patients in the TM vs NTM group had NIV usage of >4 hours/day and control of leaks.ConclusionsIn patients starting home NIV, TM with home care provider first-line support was associated with a lower therapy dropout rate at 1 year, and better compliance and leak control, compared with standard follow-up.