bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic and Phenotypic Analyses Reveal the Emergence of an Atypical Salmonella enterica Serovar Senftenberg Variant in China
Authors: Abd El Ghany Moataz , Shi Xiaolu , Li Yinghui , Ansari Hifzur R. , Hill-Cawthorne Grant A. , Ho Y. S. , Naeem Raeece , Pickard Derek , Klena John D. , Xu Xuebing , Pain Arnab , Hu Qinghua 
Published: May 2016

ABSTRACT

Human infections with
Salmonella enterica
subspecies
enterica
serovar Senftenberg are often associated with exposure to poultry flocks, farm environments, or contaminated food. The recent emergence of multidrug-resistant isolates has raised public health concerns. In this study, comparative genomics and phenotypic analysis were used to characterize 14
Salmonella
Senftenberg clinical isolates recovered from multiple outbreaks in Shenzhen and Shanghai, China, between 2002 and 2011. Single-nucleotide polymorphism analyses identified two phylogenetically distinct clades of
S
. Senftenberg, designated SC1 and SC2, harboring variations in
Salmonella
pathogenicity island 1 (SPI-1) and SPI-2 and exhibiting distinct biochemical and phenotypic signatures. Although the two variants shared the same serotype, the SC2 isolates of sequence type 14 (ST14) harbored intact SPI-1 and -2 and hence were characterized by possessing efficient invasion capabilities. In contrast, the SC1 isolates had structural deletion patterns in both SPI-1 and -2 that correlated with an impaired capacity to invade cultured human cells and also the year of their isolation. These atypical SC1 isolates also lacked the capacity to produce hydrogen sulfide. These findings highlight the emergence of atypical
Salmonella
Senftenberg variants in China and provide genetic validation that variants lacking SPI-1 and regions of SPI-2, which leads to impaired invasion capacity, can still cause clinical disease. These data have identified an emerging public health concern and highlight the need to strengthen surveillance to detect the prevalence and transmission of nontyphoidal
Salmonella
species.
Rapid Drug Susceptibility Testing of Drug-Resistant Mycobacterium tuberculosis Isolates Directly from Clinical Samples by Use of Amplicon Sequencing: a Proof-of-Concept Study
Authors: Colman Rebecca E. , Anderson Julia , Lemmer Darrin , Lehmkuhl Erik , Georghiou Sophia B. , Heaton Hannah , Wiggins Kristin , Gillece John D. , Schupp James M. , Catanzaro Donald G. , Crudu Valeriu , Cohen Ted , Rodwell Timothy C. , Engelthaler David M. 
Published: May 2016

ABSTRACT

Increasingly complex drug-resistant tuberculosis (DR-TB) is a major global health concern and one of the primary reasons why TB is now the leading infectious cause of death worldwide. Rapid characterization of a DR-TB patient's complete drug resistance profile would facilitate individualized treatment in place of empirical treatment, improve treatment outcomes, prevent amplification of resistance, and reduce the transmission of DR-TB. The use of targeted next-generation sequencing (NGS) to obtain drug resistance profiles directly from patient sputum samples has the potential to enable comprehensive evidence-based treatment plans to be implemented quickly, rather than in weeks to months, which is currently needed for phenotypic drug susceptibility testing (DST) results. In this pilot study, we evaluated the performance of amplicon sequencing of
Mycobacterium tuberculosis
DNA from patient sputum samples using a tabletop NGS technology and automated data analysis to provide a rapid DST solution (the Next Gen-RDST assay). One hundred sixty-six out of 176 (94.3%) sputum samples from the Republic of Moldova yielded complete Next Gen-RDST assay profiles for 7 drugs of interest. We found a high level of concordance of our Next Gen-RDST assay results with phenotypic DST (97.0%) and pyrosequencing (97.8%) results from the same clinical samples. Our Next Gen-RDST assay was also able to estimate the proportion of resistant-to-wild-type alleles down to mixtures of ≤1%, which demonstrates the ability to detect very low levels of resistant variants not detected by pyrosequencing and possibly below the threshold for phenotypic growth methods. The assay as described here could be used as a clinical or surveillance tool.
Comparison of Two Widely Used Human Papillomavirus Detection and Genotyping Methods, GP5+/6+-Based PCR Followed by Reverse Line Blot Hybridization and Multiplex Type-Specific E7-Based PCR
Authors: Clifford Gary M. , Vaccarella Salvatore , Franceschi Silvia , Tenet Vanessa , Umulisa M. Chantal , Tshomo Ugyen , Dondog Bolormaa , Vorsters Alex , Tommasino Massimo , Heideman Daniëlle A. M. , Snijders Peter J. F. , Gheit Tarik 
Published: May 2016

ABSTRACT
GP5+/6+-based PCR followed by reverse line blot hybridization (GP5+/6+RLB) and multiplex type-specific PCR (E7-MPG) are two human papillomavirus (HPV) genotyping methodologies widely applied in epidemiological research. We investigated their relative analytical performance in 4,662 samples derived from five studies in Bhutan, Rwanda, and Mongolia coordinated by the International Agency for Research on Cancer (IARC). A total of 630 samples were positive by E7-MPG only (13.5%), 24 were positive by GP5+/6+RLB only (0.5%), and 1,014 were positive (21.8%) by both methods. Ratios of HPV type-specific positivity of the two tests (E7-MPG:GP5+/6+RLB ratio) were calculated among 1,668 samples that were HPV positive by one or both tests. E7-MPG:GP5+/6+RLB ratios were >1 for all types and highly reproducible across populations and sample types. E7-MPG:GP5+/6+RLB ratios were highest for HPV53 (7.5) and HPV68 (7.1). HPV16 (1.6) and HPV18 (1.7) had lower than average E7-MPG:GP5+/6+RLB ratios. Among E7-MPG positive infections, median mean fluorescence intensity (MFI; a semiquantitative measure of viral load) tended to be higher among samples positive for the same virus type by GP5+/6+RLB than for those negative for the same type by GP5+/6+RLB. Exceptions, however, included HPV53, -59, and -82, for which the chances of being undetected by GP5+/6+RLB appeared to be MFI independent. Furthermore, the probability of detecting an additional type by E7-MPG was higher when another type was already detected by GP5+/6+RLB, suggesting the existence of masking effects due to competition for GP5+/6+ PCR primers. In conclusion, this analysis is not an evaluation of clinical performance but may inform choices for HPV genotyping methods in epidemiological studies, when the relative merits and dangers of sensitivity versus specificity for individual types should be considered, as well as the potential to unmask nonvaccine types following HPV vaccination.
Multiplex Real-Time PCR Assay with High-Resolution Melting Analysis for Characterization of Antimicrobial Resistance in Neisseria gonorrhoeae
Authors: Donà Valentina , Kasraian Sara , Lupo Agnese , Guilarte Yuvia N. , Hauser Christoph , Furrer Hansjakob , Unemo Magnus , Low Nicola , Endimiani Andrea 
Published: May 2016

ABSTRACT

Resistance to antibiotics used against
Neisseria gonorrhoeae
infections is a major public health concern. Antimicrobial resistance (AMR) testing relies on time-consuming culture-based methods. Development of rapid molecular tests for detection of AMR determinants could provide valuable tools for surveillance and epidemiological studies and for informing individual case management. We developed a fast (<1.5-h) SYBR green-based real-time PCR method with high-resolution melting (HRM) analysis. One triplex and three duplex reactions included two sequences for
N. gonorrhoeae
identification and seven determinants of resistance to extended-spectrum cephalosporins (ESCs), azithromycin, ciprofloxacin, and spectinomycin. The method was validated by testing 39 previously fully characterized
N. gonorrhoeae
strains, 19 commensal
Neisseria
species strains, and an additional panel of 193 gonococcal isolates. Results were compared with results of culture-based AMR determination. The assay correctly identified
N. gonorrhoeae
and the presence or absence of the seven AMR determinants. There was some cross-reactivity with nongonococcal
Neisseria
species, and the detection limit was 10
3
to 10
4
genomic DNA (gDNA) copies/reaction. Overall, the platform accurately detected resistance to ciprofloxacin (sensitivity and specificity, 100%), ceftriaxone (sensitivity, 100%; specificity, 90%), cefixime (sensitivity, 92%; specificity, 94%), azithromycin (sensitivity and specificity, 100%), and spectinomycin (sensitivity and specificity, 100%). In conclusion, our methodology accurately detects mutations that generate resistance to antibiotics used to treat gonorrhea. Low assay sensitivity prevents direct diagnostic testing of clinical specimens, but this method can be used to screen collections of gonococcal isolates for AMR more quickly than current culture-based AMR testing.
Targeted Mutagenesis of Guinea Pig Cytomegalovirus Using CRISPR/Cas9-Mediated Gene Editing
Authors: Bierle Craig J. , Anderholm Kaitlyn M. , Wang Jian Ben , McVoy Michael A. , Schleiss Mark R. 
Published: May 2016

ABSTRACT

The cytomegaloviruses (CMVs) are among the most genetically complex mammalian viruses, with viral genomes that often exceed 230 kbp. Manipulation of cytomegalovirus genomes is largely performed using infectious bacterial artificial chromosomes (BACs), which necessitates the maintenance of the viral genome in
Escherichia coli
and successful reconstitution of virus from permissive cells after transfection of the BAC. Here we describe an alternative strategy for the mutagenesis of guinea pig cytomegalovirus that utilizes clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-mediated genome editing to introduce targeted mutations to the viral genome. Transient transfection and drug selection were used to restrict lytic replication of guinea pig cytomegalovirus to cells that express Cas9 and virus-specific guide RNA. The result was highly efficient editing of the viral genome that introduced targeted insertion or deletion mutations to nonessential viral genes. Cotransfection of multiple virus-specific guide RNAs or a homology repair template was used for targeted, markerless deletions of viral sequence or to introduce exogenous sequence by homology-driven repair. As CRISPR/Cas9 mutagenesis occurs directly in infected cells, this methodology avoids selective pressures that may occur during propagation of the viral genome in bacteria and may facilitate genetic manipulation of low-passage or clinical CMV isolates.

IMPORTANCE
The cytomegalovirus genome is complex, and viral adaptations to cell culture have complicated the study of infection
in vivo
. Recombineering of viral bacterial artificial chromosomes enabled the study of recombinant cytomegaloviruses. Here we report the development of an alternative approach using CRISPR/Cas9-based mutagenesis in guinea pig cytomegalovirus, a small-animal model of congenital cytomegalovirus disease. CRISPR/Cas9 mutagenesis can introduce the same types of mutations to the viral genome as bacterial artificial chromosome recombineering but does so directly in virus-infected cells. CRISPR/Cas9 mutagenesis is not dependent on a bacterial intermediate, and defined viral mutants can be recovered after a limited number of viral genome replications, minimizing the risk of spontaneous mutation.
Effects of MF59 Adjuvant on Induction of Isotype-Switched IgG Antibodies and Protection after Immunization with T-Dependent Influenza Virus Vaccine in the Absence of CD4
+
T Cells
Authors: Ko Eun-Ju , Lee Young-Tae , Kim Ki-Hye , Jung Yu-Jin , Lee Youri , Denning Timothy L. , Kang Sang-Moo 
Published: May 2016

ABSTRACT

CD4
+
T cells play a central role in orchestrating adaptive immunity. To better understand the roles of CD4
+
T cells in the effects of adjuvants, we investigated the efficacy of a T-dependent influenza virus split vaccine with MF59 or alum in CD4 knockout (CD4KO) and wild-type (WT) mice. CD4
+
T cells were required for the induction of IgG antibody responses to the split vaccine and the effects of alum adjuvant. In contrast, MF59 was found to be highly effective in raising isotype-switched IgG antibodies to a T-dependent influenza virus split vaccine in CD4KO mice or CD4-depleted WT mice equivalent to those in intact WT mice, thus overcoming the deficiency of CD4
+
T cells in helping B cells and inducing immunity against influenza virus. Vaccination with the MF59-adjuvanted influenza virus vaccine was able to induce protective CD8
+
T cells and long-lived antibody-secreting cells in CD4KO mice. The effects of MF59 adjuvant in CD4KO mice might be associated with uric acid, inflammatory cytokines, and the recruitment of multiple immune cells at the injection site, but their cellularity and phenotypes were different from those in WT mice. These findings suggest a new paradigm of CD4-independent adjuvant mechanisms, providing the rationales to improve vaccine efficacy in infants, the elderly, immunocompromised patients, as well as healthy adults.

IMPORTANCE
MF59-adjuvanted influenza vaccines were licensed for human vaccination, but the detailed mechanisms are not fully elucidated. CD4
+
T cells are required to induce antibody isotype switching and long-term memory responses. In contrast, we discovered that MF59 was highly effective in inducing isotype-switched IgG antibodies and long-term protective immune responses to a T-dependent influenza vaccine independent of CD4
+
T cells. These findings are highly significant for the following reasons: (i) MF59 can overcome a defect of CD4
+
T cells in inducing protective immunity to vaccination with a T-dependent influenza virus vaccine; (ii) a CD4-independent pathway can be an alternative mechanism for certain adjuvants such as MF59; and (iii) this study has significant implications for improving vaccine efficacies in young children, the elderly, and immunocompromised populations.
A Genome-Wide RNA Interference Screen Identifies a Role for Wnt/β-Catenin Signaling during Rift Valley Fever Virus Infection
Authors: Harmon Brooke , Bird Sara W. , Schudel Benjamin R. , Hatch Anson V. , Rasley Amy , Negrete Oscar A. 
Published: May 2016

ABSTRACT

Rift Valley fever virus (RVFV) is an arbovirus within the
Bunyaviridae
family capable of causing serious morbidity and mortality in humans and livestock. To identify host factors involved in bunyavirus replication, we employed genome-wide RNA interference (RNAi) screening and identified 381 genes whose knockdown reduced infection. The Wnt pathway was the most represented pathway when gene hits were functionally clustered. With further investigation, we found that RVFV infection activated Wnt signaling, was enhanced when Wnt signaling was preactivated, was reduced with knockdown of β-catenin, and was blocked using Wnt signaling inhibitors. Similar results were found using distantly related bunyaviruses La Crosse virus and California encephalitis virus, suggesting a conserved role for Wnt signaling in bunyaviral infection. We propose a model where bunyaviruses activate Wnt-responsive genes to regulate optimal cell cycle conditions needed to promote efficient viral replication. The findings in this study should aid in the design of efficacious host-directed antiviral therapeutics.

IMPORTANCE
RVFV is a mosquito-borne bunyavirus that is endemic to Africa but has demonstrated a capacity for emergence in new territories (e.g., the Arabian Peninsula). As a zoonotic pathogen that primarily affects livestock, RVFV can also cause lethal hemorrhagic fever and encephalitis in humans. Currently, there are no treatments or fully licensed vaccines for this virus. Using high-throughput RNAi screening, we identified canonical Wnt signaling as an important host pathway regulating RVFV infection. The beneficial role of Wnt signaling was observed for RVFV, along with other disparate bunyaviruses, indicating a conserved bunyaviral replication mechanism involving Wnt signaling. These studies supplement our knowledge of the fundamental mechanisms of bunyavirus infection and provide new avenues for countermeasure development against pathogenic bunyaviruses.
Improving documentation of clinical care within a clinical information network: an essential initial step in efforts to understand and improve care in Kenyan hospitals
Authors: Tuti Timothy , Bitok Michael , Malla Lucas , Paton Chris , Muinga Naomi , Gathara David , Gachau Susan , Mbevi George , Nyachiro Wycliffe , Ogero Morris , Julius Thomas , Irimu Grace , English Mike 
Published: May 2016

In many low income countries health information systems are poorly equipped to provide detailed information on hospital care and outcomes. Information is thus rarely used to support practice improvement. We describe efforts to tackle this challenge and to foster learning concerning collection and use of information. This could improve hospital services in Kenya.We are developing a Clinical Information Network, a collaboration spanning 14 hospitals, policy makers and researchers with the goal of improving information available on the quality of inpatient paediatric care across common childhood illnesses in Kenya. Standardised data from hospitals' paediatric wards are collected using non-commercial and open source tools. We have implemented procedures for promoting data quality which are performed prior to a process of semi-automated analysis and routine report generation for hospitals in the network.In the first phase of the Clinical Information Network, we collected data on over 65 000 admission episodes. Despite clinicians' initial unfamiliarity with routine performance reporting, we found that, as an initial focus, both engaging with each hospital and providing them information helped improve the quality of data and therefore reports. The process has involved mutual learning and building of trust in the data and should provide the basis for collaborative efforts to improve care, to understand patient outcome, and to evaluate interventions through shared learning.We have found that hospitals are willing to support the development of a clinically focused but geographically dispersed Clinical Information Network in a low-income setting. Such networks show considerable promise as platforms for collaborative efforts to improve care, to provide better information for decision making, and to enable locally relevant research.
Reactions and coping strategies in lay rescuers who have provided CPR to out-of-hospital cardiac arrest victims: a qualitative study
Authors: Mathiesen Wenche Torunn , Bjørshol Conrad Arnfinn , Braut Geir Sverre , Søreide Eldar 
Published: May 2016

ObjectiveCardiopulmonary resuscitation (CPR) provided by community citizens is of paramount importance for out-of-hospital cardiac arrest (OHCA) victims' survival. Fortunately, CPR rates by community citizens seem to be rising. However, the experience of providing CPR is rarely investigated. The aim of this study was to explore reactions and coping strategies in lay rescuers who have provided CPR to OHCA victims.Methods, participantsThis is a qualitative study of 20 lay rescuers who have provided CPR to 18 OHCA victims. We used a semistructured interview guide focusing on their experiences after providing CPR.SettingThe study was conducted in the Stavanger region of Norway, an area with very high bystander CPR rates.ResultsThree themes emerged from the interview analysis: concern, uncertainty and coping strategies. Providing CPR had been emotionally challenging for all lay rescuers and, for some, had consequences in terms of family and work life. Several lay rescuers experienced persistent mental recurrences of the OHCA incident and had concerns about the outcome for the cardiac arrest victim. Unknown or fatal outcomes often caused feelings of guilt and were particularly difficult to handle. Several reported the need to be acknowledged for their CPR attempts. Health-educated lay rescuers seemed to be less affected than others. A common coping strategy was confiding in close relations, preferably the health educated. However, some required professional help to cope with the OHCA incident.ConclusionsLay rescuers experience emotional and social challenges, and some struggle to cope in life after providing CPR in OHCA incidents. Experiencing a positive patient outcome and being a health-educated lay rescuer seem to mitigate concerns. Common coping strategies are attempts to reduce uncertainty towards patient outcome and own CPR quality. Further studies are needed to determine whether an organised professional follow-up can mitigate the concerns and uncertainty of lay rescuers.
School and seasonality in youth suicide: evidence from Japan
Authors: Matsubayashi Tetsuya , Ueda Michiko , Yoshikawa Kanako 
Published: May 2016

BackgroundSeasonality in youth suicide has been speculated to be associated with the school calendar, as it tends to increase at the beginning of the academic year or after a long break, but robust empirical evidence remains scarce.MethodsWe examined the nationwide death records in the Vital Statistics of Japan to investigate the seasonal patterns of suicide among youth. Our data set included 108 968 suicides by individuals who died at 6–26 years of age between 1974 and 2014 in Japan. The daily frequencies of death were plotted against the Japanese school calendar, which has little regional and temporal variations. We also estimated a Poisson regression model to uncover the cyclical patterns of suicide deaths.ResultsWe found that the frequencies of suicide by middle school students (ages 12–15 years) and high school students (ages 15–18 years) sharply increased around the dates when a school session began in April and September. These tended to be low during school breaks. The results of regression analysis suggested middle school students were more than twice as likely to die by suicide when the summer break ended and the second semester began, compared with the baseline week in July. Similarly, the frequency of suicide for high school students also increased by ∼40% at the end of the summer break. Importantly, no such pattern was found for those aged 18–26 years.ConclusionsOur findings strongly indicate that the cyclical pattern of youth suicide is closely related to the school calendar.
Nest defense behaviour of four raptor species (osprey, bald eagle, ferruginous hawk, and red-tailed hawk) to a novel aerial intruder – a small rotary-winged drone
Authors: Junda James H. , Greene Erick , Zazelenchuk Dan , Bird David M. 
Published: May 2016

A small rotary-winged unmanned aerial vehicle (UAV) was flown above the nests of four raptor species: osprey (Pandion haliaetus), bald eagle (Haliaeetus leucocephalus), ferruginous hawk (Buteo regalis), and red-tailed hawk (B. jamaicensis) to document the parental nest defense response to the aircraft. Adult behaviour was documented with a voice recorder and an ethogram, starting ~100 m distant from the nest and continuing until the base of the nest was reached, the survey completed, and the nest area exited. All adult movements and vocalizations were recorded with distance of bird and researchers from the nest when a given behaviour occurred. Ospreys showed the strongest nest defense response followed by ferruginous hawks and red-tailed hawks with bald eagles showing the least aggressive response. Ospreys showed no greater response to the UAV in the air near the nest than to researchers simply standing at the base of the nest structure, while bald eagles showed a significantly higher response to the aircraft than researchers at the nest base. Although aggression varied, no species showed aggression at levels that would discourage the use of UAVs to survey raptor nests. When a proper flight technique is adopted, UAVs can offer a useful tool for surveying raptor nests.