bluuebunny/crossref_metadata_2025_split huggingface dataset:
A New Niche for Anoxygenic Phototrophs as Endoliths
Authors: Roush Daniel , Couradeau Estelle , Guida Brandon , Neuer Susanne , Garcia-Pichel Ferran 
Published: December 2017

ABSTRACTAnoxygenic phototrophic bacteria (APBs) occur in a wide range of aquatic habitats, from hot springs to freshwater lakes and intertidal microbial mats. Here, we report the discovery of a novel niche for APBs: endoliths within marine littoral carbonates. In a study of 40 locations around Isla de Mona, Puerto Rico, and Menorca, Spain, 16S rRNA high-throughput sequencing of endolithic community DNA revealed the presence of abundant phylotypes potentially belonging to well-known APB clades. Anad hocphylogenetic classification of these sequences enabled us to refine the assignments more stringently. Even then, all locations contained such putative APBs, often reaching a significant proportion of all phototrophic sequences. In fact, in some 20% of samples, their contribution exceeded that of oxygenic phototrophs, previously regarded as the major type of endolithic microbe in carbonates. The communities contained representatives of APBs in theChloroflexales, various proteobacterial groups, andChlorobi. The most abundant phylotypes varied with geography: on Isla de Mona,RoseiflexusandChlorothrix-related phylotypes dominated, whereas those related toErythrobacterwere the most common in Menorca. The presence of active populations of APBs was corroborated through an analysis of photopigments: bacteriochlorophylls were detected in all samples, bacteriochlorophyllcandabeing most abundant. We discuss the potential metabolism and geomicrobial roles of endolithic APBs. Phylogenetic inference suggests that APBs may be playing a role as photoheterotrophs, adding biogeochemical complexity to our understanding of such communities. Given the global extent of coastal carbonate platforms, they likely represent a very large and unexplored habitat for APBs.IMPORTANCEEndolithic microbial communities from carbonates, which have been explored for over 2 centuries in predominantly naturalistic studies, were thought to be primarily composed of eukaryotic algae and cyanobacteria. Our report represents a paradigm shift in this regard, at least for the marine environment, demonstrating the presence of ubiquitous and abundant populations of APBs in this habitat. It raises questions about the role of these organisms in the geological dynamics of coastal carbonates, including coral reefs.
The Emergency Medical Service Microbiome
Authors: Hudson Andrew J. , Glaister Graeme D. , Wieden Hans-Joachim 
Published: December 2017

ABSTRACT

Emergency medical services (EMS) personnel are an integral component of the health care framework and function to transport patients from various locations to and between care facilities. In addition to physical injury, EMS personnel are expected to be at high risk to acquire and transmit health care-associated infections (HAIs) in the workplace. However, currently, little is known about EMS biosafety risk factors and the epidemiological contribution of EMS to pathogen transmission within and outside the health care sector. Health care facility microbiomes contain diverse bacterial, fungal, and viral pathogens that cause over 1.7 million HAIs each year in the United States alone. While hospital microbiomes have been relatively well studied, there is scant information about EMS infrastructure and equipment microbiomes or the role(s) they play in HAI transmission between health care facilities. We review recent literature investigating the microbiome of ambulances and other EMS service facilities which consistently identify antibiotic-resistant pathogens causing HAIs, including methicillin-resistant
Staphylococcus aureus
(MRSA), vancomycin-resistant
Enterococcus
, and
Klebsiella pneumoniae
. Our review provides evidence that EMS microbiomes are dynamic and important pathogen reservoirs, and it underscores the need for more widespread and in-depth microbiome studies to elucidate patterns of pathogen transmission. We discuss emerging DNA sequencing technologies and other methods that can be applied to characterize and mitigate EMS biosafety risks in the future. Understanding the complex interplay between EMS and hospital microbiomes will provide key insights into pathogen transmission mechanisms and identify strategies to minimize HAIs and community infection.
Genome Sequences of 19 Rhodococcus erythropolis Cluster CA Phages
Authors: Bonilla J. Alfred , Isern Sharon , Findley Ann M. , Klyczek Karen K. , Michael Scott F. , Saha Margaret S. , Buchser William J. , Forsyth Mark H. , Paudel Sudip , Gissendanner Christopher R. , Wiedemeier Allison M. D. , Alonzo Fernanda L. ,   University of Wisconsin–River Falls SEA-PHAGES,   Florida Gulf Coast University SEA-PHAGES,   University of Louisiana–Monroe SEA-PHAGES,   College of William & Mary SEA-PHAGES, Garlena Rebecca A. , Russell Daniel A. , Pope Welkin H. , Cresawn Steven G. , Jacobs-Sera Deborah , Hatfull Graham F. 
Published: December 2017

ABSTRACT

We report the complete genome sequences of 19 cluster CA bacteriophages isolated from environmental samples using
Rhodococcus erythropolis
as a host. All of the phages are
Siphoviridae
, have similar genome lengths (46,314 to 46,985 bp) and G+C contents (58.5 to 58.8%), and share nucleotide sequence similarity.
Full-Length Genome Sequence of a Chikungunya Virus Isolate from the 2017 Autochthonous Outbreak, Lazio Region, Italy
Authors: Carletti Fabrizio , Marsella Patrizia , Colavita Francesca , Meschi Silvia , Lalle Eleonora , Bordi Licia , Di Lallo Domenico , Panella Vincenzo , Di Caro Antonino , Nicastri Emanuele , Scognamiglio Paola , Lanini Simone , Vairo Francesco , Capobianchi Maria R. , Ippolito Giuseppe , Castilletti Concetta 
Published: December 2017

ABSTRACT

We report here the genome sequence of a human chikungunya virus isolate from the ongoing autochthonous outbreak in central Italy. The sequence (East-Central-South African lineage, Indian Ocean sublineage), which is similar to recent sequences from Pakistan and India, shows E1 and E2 signatures of strains whose main mosquito vector is
Aedes aegypti
, although
Aedes albopictus
is the vector in Italy.
Complete Genome Sequences of Plasmid-Bearing Campylobacter coli and Campylobacter jejuni Strains Isolated from Retail Chicken Liver
Authors: Marasini Daya , Fakhr Mohamed K. 
Published: December 2017

ABSTRACT

Complete genome sequences of
Campylobacter coli
strains WA333, YF2105, BG2108, MG1116, and BP3183 and
Campylobacter jejuni
strain IF1100 isolated from retail chicken liver showed the presence of 1,841,551-, 1,687,232-, 1,695,638-, 1,665,146-, 1,695,360-, and 1,744,171-bp circular chromosomes, respectively. These isolates also contained plasmids ranging in size from 5,209 to 55,122 bp.
Molecular Methods for Detection of Antimicrobial Resistance
Authors: Anjum Muna F. , Zankari Ea , Hasman Henrik 
Published: December 2017

ABSTRACT
The increase in bacteria harboring antimicrobial resistance (AMR) is a global problem because there is a paucity of antibiotics available to treat multidrug-resistant bacterial infections in humans and animals. Detection of AMR present in bacteria that may pose a threat to veterinary and public health is routinely performed using standardized phenotypic methods. Molecular methods are often used in addition to phenotypic methods but are set to replace them in many laboratories due to the greater speed and accuracy they provide in detecting the underlying genetic mechanism(s) for AMR. In this article we describe some of the common molecular methods currently used for detection of AMR genes. These include PCR, DNA microarray, whole-genome sequencing and metagenomics, and matrix-assisted laser desorption ionization–time of flight mass spectrometry. The strengths and weaknesses of these methods are discussed, especially in the context of implementing them for routine surveillance activities on a global scale for mitigating the risk posed by AMR worldwide. Based on current popularity and ease of use, PCR and single-isolate whole-genome sequencing seem irreplaceable.
Antimicrobial Resistance inCorynebacteriumspp.,Arcanobacteriumspp., andTrueperella pyogenes
Authors: Feßler Andrea T. , Schwarz Stefan 
Published: December 2017

ABSTRACTThere is currently only limited information on the antimicrobial susceptibility and resistance ofCorynebacteriumspp.,Arcanobacteriumspp., andTrueperella pyogenesfrom animals. The comparability of the data is hampered by the use of different antimicrobial susceptibility testing methods and interpretive criteria. To date, standard broth microdilution methods and clinical breakpoints that are approved by the Clinical and Laboratory Standards Institute and are applicable toCorynebacteriumspp.,Arcanobacteriumspp., andT. pyogenesare available. The lack of species-specific clinical breakpoints for the different animal species reduces the explanatory power of the data. Among the isolates of the three genera, elevated MICs for different classes of antimicrobial agents (e.g., β-lactams, macrolides, lincosamides, tetracyclines, aminoglycosides, phenicols, sulfonamides/diaminopyrimidines, and fluoroquinolones) have been described. The most comprehensive data set is available forT. pyogenes, which also includes information about genes and mutations involved in antimicrobial resistance. InT. pyogenesisolates, the macrolide-lincosamide-streptogramin B resistance geneserm(B) anderm(X) were identified. Tetracycline resistance inT. pyogeneswas based on the resistance genestet(W),tet(Z), andtet(33), whereas the aminoglycoside resistance genesaacC,aadA1,aadA2,aadA5,aadA24, andaadBhave been described inT. pyogenes. So far, only single genes conferring either phenicol resistance (cmlA6), trimethoprim resistance (dfrB2a), or β-lactam resistance (blaP1) are known to occur inT. pyogenesisolates. Various 23S rRNA mutations, including A2058T, A2058G, and G2137C, were identified in macrolide/lincosamide-resistantT. pyogenes.
Workplace violence, psychological stress, sleep quality and subjective health in Chinese doctors: a large cross-sectional study
Authors: Sun Tao , Gao Lei , Li Fujun , Shi Yu , Xie Fengzhe , Wang Jinghui , Wang Shuo , Zhang Shue , Liu Wenhui , Duan Xiaojian , Liu Xinyan , Zhang Zhong , Li Li , Fan Lihua 
Published: December 2017

BackgroundWorkplace violence (WPV) against healthcare workers is known as violence in healthcare settings and referring to the violent acts that are directed towards doctors, nurses or other healthcare staff at work or on duty. Moreover, WPV can cause a large number of adverse outcomes. However, there is not enough evidence to test the link between exposure to WPV against doctors, psychological stress, sleep quality and health status in China.ObjectivesThis study had three objectives: (1) to identify the incidence rate of WPV against doctors under a new classification, (2) to examine the association between exposure to WPV, psychological stress, sleep quality and subjective health of Chinese doctors and (3) to verify the partial mediating role of psychological stress.DesignA cross-sectional online survey study.SettingThe survey was conducted among 1740 doctors in tertiary hospitals, 733 in secondary hospital and 139 in primary hospital across 30 provinces of China.ParticipantsA total of 3016 participants were invited. Ultimately, 2617 doctors completed valid questionnaires. The effective response rate was 86.8%.ResultsThe results demonstrated that the prevalence rate of exposure to verbal abuse was the highest (76.2%), made difficulties (58.3%), smear reputation (40.8%), mobbing behaviour (40.2%), intimidation behaviour (27.6%), physical violence (24.1%) and sexual harassment (7.8%). Exposure to WPV significantly affected the psychological stress, sleep quality and self-reported health of doctors. Moreover, psychological stress partially mediated the relationship between work-related violence and health damage.ConclusionIn China, most doctors have encountered various WPV from patients and their relatives. The prevalence of three new types of WPV have been investigated in our study, which have been rarely mentioned in past research. A safer work environment for Chinese healthcare workers needs to be provided to minimise health threats, which is a top priority for both government and society.
Benefits of probiotics in preterm neonates in low-income and medium-income countries: a systematic review of randomised controlled trials
Authors: Deshpande Girish , Jape Gayatri , Rao Shripada , Patole Sanjay 
Published: December 2017

ObjectiveAlthough there is an overall reduction in underfive mortality rate, the progress in reducing neonatal mortality rate has been very slow. Over the last 20 years, preterm births have steadily increased in low-income and medium-income countries (LMICs) particularly in sub-Saharan Africa and South Asia. Preterm birth is associated with increased mortality and morbidity, particularly in LMICs. Based on systematic reviews of randomised controlled trials (RCTs), many neonatal units in high-income countries have adopted probiotics as standard of care for preterm neonates. We aimed to systematically review the safety and efficacy of probiotics in reducing mortality and morbidity in preterm neonates in LMICs.DesignSystematic review and meta-analysis of RCTs.Data sourcesMedline, Embase, Cochrane Central Register of Controlled Trials, Cumulative Index of Nursing and Allied Health Literature and E-abstracts from Pediatric Academic Society meetings and other paediatric and neonatal conference proceedings were searched in January 2017.Eligibility criteriaRCTs comparing probiotics versus placebo/no probiotic in preterm neonates (gestation<37 weeks) conducted in LMICs.ResultsTotal 23 (n=4783) RCTs from 4 continents and 10 LMICs were eligible for inclusion in the meta-analysis using fixed effect model. The risk of necrotising enterocolitis (NEC greater than or equal to stage II) (risk ratio (RR) 0.46 (95% CI 0.34 to 0.61), P<0.00001, numbers needed to treat (NNT) 25 (95% CI 20 to 50)), late-onset sepsis (LOS) (RR 0.80 (95% CI 0.71 to 0.91), P=0.0009, NNT 25 (95% CI 17 to 100)) and all-cause mortality (RR 0.73 (95% CI 0.59 to 0.90), P=0.003, NNT 50 (95% CI 25 to 100)) were significantly lower in probiotic supplemented neonates. The results were significant on random effects model analysis and after excluding studies with high risk of bias. No significant adverse effects were reported.ConclusionProbiotics have significant potential to reduce mortality and morbidity (eg, NEC, LOS) in preterm neonates in LMICs.
Evaluation of cognitive load and emotional states during multidisciplinary critical care simulation sessions
Authors: Pawar Swapnil , Jacques Theresa , Deshpande Kush , Pusapati Raju , Meguerdichian Michael J 
Published: December 2017

BackgroundThe simulation in critical care setting involves a heterogeneous group of participants with varied background and experience. Measuring the impacts of simulation on emotional state and cognitive load in this setting is not often performed. The feasibility of such measurement in the critical care setting needs further exploration.MethodsMedical and nursing staff with varying levels of experience from a tertiary intensive care unit participated in a standardised clinical simulation scenario. The emotional state of each participant was assessed before and after completion of the scenario using a validated eight-item scale containing bipolar oppositional descriptors of emotion. The cognitive load of each participant was assessed after the completion of the scenario using a validated subjective rating tool.ResultsA total of 103 medical and nursing staff participated in the study. The participants felt more relaxed (−0.28±1.15 vs 0.14±1, P<0.005; d=0.39), excited (0.25±0.89 vs 0.55±0.92, P<0.005, d=0.35) and alert (0.85±0.87 vs 1.28±0.73, P<0.00001, d=0.54) following simulation. There was no difference in the mean scores for the remaining five items. The mean cognitive load for all participants was 6.67±1.41. There was no significant difference in the cognitive loads among medical staff versus nursing staff (6.61±2.3 vs 6.62±1.7; P>0.05).ConclusionA well-designed complex high fidelity critical care simulation scenario can be evaluated to identify the relative cognitive load of the participants’ experience and their emotional state. The movement of learners emotionally from a more negative state to a positive state suggests that simulation can be an effective tool for improved knowledge transfer and offers more opportunity for dynamic thinking.
How are junior doctors managing patients with self-limiting illnesses at their first presentation? A video vignette study
Authors: D’Souza Eugene , Krejany Catherine , Meng Rosie , Jiwa Moyez 
Published: December 2017

AbstractPurposeTo conduct a video vignette survey of medical students and doctors investigating test ordering for patients presenting with self-limiting or minor illness.MethodsParticipants were shown six video vignettes of common self-limiting illnesses and invited to devise investigation and management plans for the patients’ current presentation. The number of tests ordered was compared with those recommended by an expert panel. A Theory of Planned Behaviour Questionnaire explored participants’ beliefs and attitudes about ordering tests in the context of self-limiting illness.ResultsParticipants (n=61) were recruited from across Australia. All participants ordered at least one test that was not recommended by the experts in most cases. Presentations that focused mainly on symptoms (eg, in cases with bowel habit disturbance and fatigue) resulted in more tests being ordered. A test not recommended by experts was ordered on 54.9% of occasions. With regard to attitudes to test ordering, junior doctors were strongly influenced by social norms. The number of questionable tests ordered in this survey of 366 consultations has a projected cost of $17 000.ConclusionsThis study suggests that there is some evidence of questionable test ordering by these participants with significant implications for costs to the health system. Further research is needed to explore the extent and reasons for test ordering by junior doctors across a range of clinical settings.
Laser Balloon or Wide-Area Circumferential Irrigated Radiofrequency Ablation for Persistent Atrial Fibrillation
Authors: Schmidt Boris , Neuzil Petr , Luik Armin , Osca Asensi Joaquin , Schrickel Jan Wilko , Deneke Thomas , Bordignon Stefano , Petru Jan , Merkel Matthias , Sediva Lucie , Klostermann Annemarie , Perrotta Laura , Cano Oscar , Chun K.R. Julian 
Published: December 2017

Background
Pulmonary vein isolation is the cornerstone of ablation for persistent atrial fibrillation (AF). The role of balloon catheters in this patient population remains ill defined. We sought to compare efficacy and safety of the laser balloon (LB) with wide-area circumferential pulmonary vein isolation using irrigated radiofrequency current (RF) ablation and 3-dimensional mapping.

Methods and Results

In 6 European centers, patients with persistent AF were prospectively randomized. Follow-up included 3-day Holter ECG recordings and office visits at 3, 6, and 12 months. The primary efficacy end point was freedom from AF between 90 and 365 days after a single ablation. The primary safety end point was the incidence of any periprocedural complications. Of 152 enrolled patients, 134 (n=68 LB and 66 RF; 63% men; mean age, 66+10 years) with persistent AF (median AF history, 14 months; Q1–Q3, 7–36 months) underwent pulmonary vein isolation and completed the entire follow-up. Baseline parameters were similar in both groups. Procedure and fluoroscopy times were similar in both groups (135±38 and 14±9 minutes (LB) versus 128±51 and 11±9 minutes). The primary efficacy end point was met by 71.2% versus 69.3%, in the LB and RF groups, respectively (
P
=0.40). In the LB group, stroke (n=1), a false aneurysm (n=1), and phrenic nerve palsy (n=1) were observed. In the RF group, 2 patients developed a false aneurysm, and 1 patient needed surgical repair.

Conclusions
An LB-guided strategy was associated with similar efficacy as wide-area circumferential pulmonary vein isolation using irrigated RF in patients with persistent AF.

Clinical Trial Registration

https://www.clinicaltrials.org
. Unique identifier: NCT01863472.
Effect of Losartan on Right Ventricular Dysfunction
Authors: Bokma Jouke P. , Winter Michiel M. , van Dijk Arie P. , Vliegen Hubert W. , van Melle Joost P. , Meijboom Folkert J. , Post Martijn C. , Berbee Jacqueline K. , Boekholdt S. Matthijs , Groenink Maarten , Zwinderman Aeilko H. , Mulder Barbara J.M. , Bouma Berto J. 
Published: December 2017

Background:
The effect of angiotensin II receptor blockers on right ventricular (RV) function is still unknown. Angiotensin II receptor blockers are beneficial in patients with acquired left ventricular dysfunction, and recent findings have suggested a favorable effect in symptomatic patients with systemic RV dysfunction. The current study aimed to determine the effect of losartan, an angiotensin II receptor blocker, on subpulmonary RV dysfunction in adults after repaired tetralogy of Fallot.

Methods:
The REDEFINE trial (Right Ventricular Dysfunction in Tetralogy of Fallot: Inhibition of the Renin-Angiotensin-Aldosterone System) is an investigator-initiated, multicenter, prospective, 1:1 randomized, double-blind, placebo-controlled study. Adults with repaired tetralogy of Fallot and RV dysfunction (RV ejection fraction [EF] <50%) but without severe valvular dysfunction were eligible. Patients were randomly assigned between losartan (150 mg daily) and placebo with target treatment duration between 18 and 24 months. The primary outcome was RV EF change, determined by cardiovascular MRI in intention-to-treat analysis.

Results:

Of 95 included patients, 47 patients received 150 mg losartan daily (age, 38.0±12.4 years; 74% male), and 48 patients received placebo (age, 40.6±11.4 years; 63% male). Overall, RV EF did not change in patients allocated to losartan (n=42) (44.4±5.1% to 45.2±5.0%) and placebo (n=46) (43.2±6.3% to 43.6±6.9%). Losartan did not significantly improve RV EF in comparison with placebo (+0.51%; 95% confidence interval, –1.0 to +2.0;
P
=0.50). No significant treatment effects were found on secondary outcomes: left ventricular EF, peak aerobic exercise capacity, and N-terminal pro–brain natriuretic peptide (
P
>0.30 for all). In predefined subgroup analyses, losartan did not have a statistically significant impact on RV EF in subgroups with symptoms, restrictive RV, RV EF<40%, pulmonary valve replacement, or QRS fragmentation. However, in a post hoc analysis, losartan was associated with improved RV EF in a subgroup (n=30) with nonrestrictive RV and incomplete remodeling (QRS fragmentation and previous pulmonary valve replacement) (+2.7%; 95% confidence interval, +0.1 to +5.4;
P
=0.045).

Conclusions:
Losartan had no significant effect on RV dysfunction or secondary outcome parameters in repaired tetralogy of Fallot. Future larger studies may determine whether there might be a role for losartan in specific vulnerable subgroups.

Clinical Trial Registration:

URL:
https://www.clinicaltrials.gov
. Unique identifier: NCT02010905.