bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Decade of Development of Chromogenic Culture Media for Clinical Microbiology in an Era of Molecular Diagnostics
Authors: Perry John D. 
Published: January 2017

SUMMARY

In the last 25 years, chromogenic culture media have found widespread application in diagnostic clinical microbiology. In the last decade, the range of media available to clinical laboratories has expanded greatly, allowing specific detection of additional pathogens, including
Pseudomonas aeruginosa
, group B streptococci,
Clostridium difficile
,
Campylobacter
spp., and
Yersinia enterocolitica
. New media have also been developed to screen for pathogens with acquired antimicrobial resistance, including vancomycin-resistant enterococci, carbapenem-resistant
Acinetobacter
spp., and
Enterobacteriaceae
with extended-spectrum β-lactamases and carbapenemases. This review seeks to explore the utility of chromogenic media in clinical microbiology, with particular attention given to media that have been commercialized in the last decade. The impact of laboratory automation and complementary technologies such as matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) is also assessed. Finally, the review also seeks to demarcate the role of chromogenic media in an era of molecular diagnostics.
Multicenter Comparison Study of both Analytical and Clinical Performance across Four Roche Hepatitis C Virus RNA Assays Utilizing Different Platforms
Authors: Vermehren Johannes , Stelzl Evelyn , Maasoumy Benjamin , Michel-Treil Veronique , Berkowski Caterina , Marins Ed G. , Paxinos Ellen E. , Marino Enrique , Wedemeyer Heiner , Sarrazin Christoph , Kessler Harald H. 
Published: January 2017

ABSTRACT

The efficacy of antiviral treatment for chronic hepatitis C virus (HCV) infection is determined by measuring HCV RNA at specific time points throughout therapy using highly sensitive and accurate HCV RNA assays. This study compared the performances of two recently developed real-time PCR HCV RNA assays, cobas HCV for use on the cobas 6800/8800 systems (cobas 6800/8800 HCV) and cobas HCV for use on the cobas 4800 system (cobas 4800 HCV), with those of two established assays, the Cobas AmpliPrep/Cobas TaqMan HCV quantitative test, version 2 (CAP/CTM v2) and the Cobas TaqMan HCV test, version 2 for use with the High Pure system (HPS/CTM v2). The limits of detection (LODs) and linearity at lower concentrations (5 to 1000 IU/ml) were assessed for cobas 6800/8800 HCV and cobas 4800 HCV using WHO standard traceable panels representing HCV genotypes (GT) 1 to 4. Pairwise assay comparisons were also performed using 245 clinical samples representing HCV GT 1 to GT 4. Results from cobas 6800/8800 HCV and cobas 4800 HCV were linear at low HCV RNA concentrations (<0.3 log
10
IU/ml difference between expected and observed results) with LODs of 8.2 IU/ml and 11.7 IU/ml, respectively, for GT 1. The new assays showed excellent agreement with results from CAP/CTM v2 and HPS/CTM v2 in samples with quantifiable viral loads. The concordances using the 6 million IU/ml cutoff were high among all four assays (90 to 94%). In conclusion, the cobas 6800/8800 HCV and cobas 4800 HCV tests are sensitive and linear and correlate well with the established Roche assays used in clinical practice.
Rising Stakes for Health Care-Associated Infection Prevention: Implications for the Clinical Microbiology Laboratory
Authors: Diekema Daniel J. 
Published: January 2017

ABSTRACT
Health care-associated infection (HAI) rates are subject to public reporting and are linked to hospital reimbursement from the Centers for Medicare and Medicaid Services (CMS). The increasing pressure to lower HAI rates comes at a time when advances in the clinical microbiology laboratory (CML) provide more-precise and -sensitive tests, altering HAI detection in ways that may increase reported HAI rates. I review how changing CML practices can impact HAI rates and how the financial implications of HAI metrics may produce pressure to change diagnostic testing practices. Finally, I provide suggestions for how to respond to this rapidly changing environment.
Conserved Interaction of Lentiviral Vif Molecules with HIV-1 Gag and Differential Effects of Species-Specific Vif on Virus Production
Authors: Zheng Wenwen , Ling Limian , Li Zhaolong , Wang Hong , Rui Yajuan , Gao Wenying , Wang Shaohua , Su Xing , Wei Wei , Yu Xiao-Fang 
Published: January 2017

ABSTRACT

The virion infectivity factor (Vif) open reading frame is conserved among most lentiviruses. Vif molecules contribute to viral replication by inactivating host antiviral factors, the APOBEC3 cytidine deaminases. However, various species of lentiviral Vif proteins have evolved different strategies for overcoming host APOBEC3. Whether different species of lentiviral Vif proteins still preserve certain common features has not been reported. Here, we show for the first time that diverse lentiviral Vif molecules maintain the ability to interact with the human immunodeficiency virus type 1 (HIV-1) Gag precursor (Pr55
Gag
) polyprotein. Surprisingly, bovine immunodeficiency virus (BIV) Vif, but not HIV-1 Vif, interfered with HIV-1 production and viral infectivity even in the absence of APOBEC3. Further analysis revealed that BIV Vif demonstrated an enhanced interaction with Pr55
Gag
compared to that of HIV-1 Vif, and BIV Vif defective for the Pr55
Gag
interaction lost its ability to inhibit HIV-1. The C-terminal region of capsid (CA) and the p2 region of Pr55
Gag
, which are important for virus assembly and maturation, were involved in the interaction. Transduction of CD4
+
T cells with BIV Vif blocked HIV-1 replication. Thus, the conserved Vif-Pr55
Gag
interaction provides a potential target for the future development of antiviral strategies.

IMPORTANCE
The conserved Vif accessory proteins of primate lentiviruses HIV-1, simian immunodeficiency virus (SIV), and BIV all form ubiquitin ligase complexes to target host antiviral APOBEC3 proteins for degradation, with different cellular requirements and using different molecular mechanisms. Here, we demonstrate that BIV Vif can interfere with HIV-1 Gag maturation and suppress HIV-1 replication through interaction with the precursor of the Gag (Pr55
Gag
) of HIV-1 in virus-producing cells. Moreover, the HIV-1 and SIV Vif proteins are conserved in terms of their interactions with HIV-1 Pr55
Gag
although HIV-1 Vif proteins bind Pr55
Gag
less efficiently than those of BIV Vif. Our research not only sheds new light on this feature of these conserved lentiviral Vif proteins but also provides a formerly unrecognized target for the development of antiviral strategies. Since increasing the Vif-Pr55
Gag
interaction could potentially suppress virus proliferation, this approach could offer a new strategy for the development of HIV inhibitors.
The FACT Complex Promotes Avian Leukosis Virus DNA Integration
Authors: Winans Shelby , Larue Ross C. , Abraham Carly M. , Shkriabai Nikolozi , Skopp Amelie , Winkler Duane , Kvaratskhelia Mamuka , Beemon Karen L. 
Published: January 2017

ABSTRACT

All retroviruses need to integrate a DNA copy of their genome into the host chromatin. Cellular proteins regulating and targeting lentiviral and gammaretroviral integration in infected cells have been discovered, but the factors that mediate alpharetroviral avian leukosis virus (ALV) integration are unknown. In this study, we have identified the FACT protein complex, which consists of SSRP1 and Spt16, as a principal cellular binding partner of ALV integrase (IN). Biochemical experiments with purified recombinant proteins show that SSRP1 and Spt16 are able to individually bind ALV IN, but only the FACT complex effectively stimulates ALV integration activity
in vitro
. Likewise, in infected cells, the FACT complex promotes ALV integration activity, with proviral integration frequency varying directly with cellular expression levels of the FACT complex. An increase in 2-long-terminal-repeat (2-LTR) circles in the depleted FACT complex cell line indicates that this complex regulates the ALV life cycle at the level of integration. This regulation is shown to be specific to ALV, as disruption of the FACT complex did not inhibit either lentiviral or gammaretroviral integration in infected cells.

IMPORTANCE
The majority of human gene therapy approaches utilize HIV-1- or murine leukemia virus (MLV)-based vectors, which preferentially integrate near genes and regulatory regions; thus, insertional mutagenesis is a substantial risk. In contrast, ALV integrates more randomly throughout the genome, which decreases the risks of deleterious integration. Understanding how ALV integration is regulated could facilitate the development of ALV-based vectors for use in human gene therapy. Here we show that the FACT complex directly binds and regulates ALV integration efficiency
in vitro
and in infected cells.
Monoclonal Antibodies Specific for the V2, V3, CD4-Binding Site, and gp41 of HIV-1 Mediate Phagocytosis in a Dose-Dependent Manner
Authors: Musich Thomas , Li Liuzhe , Liu Lily , Zolla-Pazner Susan , Robert-Guroff Marjorie , Gorny Miroslaw K. 
Published: January 2017

ABSTRACTIn light of the weak or absent neutralizing activity mediated by anti-V2 monoclonal antibodies (MAbs), we tested whether they can mediate Ab-dependent cellular phagocytosis (ADCP), which is an important element of anti-HIV-1 immunity. We tested six anti-V2 MAbs and compared them with 21 MAbs specific for V3, the CD4-binding site (CD4bs), and gp41 derived from chronically HIV-1-infected individuals and produced by hybridoma cells. ADCP activity was measured by flow cytometry using uptake by THP-1 monocytic cells of fluorescent beads coated with gp120, gp41, BG505 SOSIP.664, or BG505 DS-SOSIP.664 complexed with MAbs. The measurement of ADCP activity by the area under the curve showed significantly higher activity of anti-gp41 MAbs than of the members of the three other groups of MAbs tested using beads coated with monomeric gp41 or gp120; anti-V2 MAbs were dominant compared to anti-V3 and anti-CD4bs MAbs against clade C gp120ZM109. ADCP activity mediated by V2 and V3 MAbs was positive against stabilized DS-SOSIP.664 trimer but negligible against SOSIP.664 targets, suggesting that a closed envelope conformation better exposes the variable loops. Two IgG3 MAbs against the V2 and V3 regions displayed dominant ADCP activity compared to a panel of IgG1 MAbs. This superior ADCP activity was confirmed when two of three recombinant IgG3 anti-V2 MAbs were compared to their IgG1 counterparts. The study demonstrated dominant ADCP activity of anti-gp41 against monomers but not trimers, with some higher activity of anti-V2 MAbs than of anti-V3 and anti-CD4bs MAbs. The ability to mediate ADCP suggests a mechanism by which anti-HIV-1 envelope Abs can contribute to protective efficacy.IMPORTANCEAnti-V2 antibodies (Abs) correlated with reduced risk of HIV-1 infection in recipients of the RV144 vaccine, suggesting that they play a protective role, but a mechanism providing such protection remains to be determined. The rare and weak neutralizing activities of anti-V2 MAbs prompted us to study Fc-mediated activities. We compared anti-V2 MAbs with other MAbs specific for V3, CD4bs, and gp41 for Ab-dependent cellular phagocytosis (ADCP) activity, implicated in protective immunity. The anti-V2 MAbs displayed stronger activity than other anti-gp120 MAbs in screening against one of two gp120s and against DS-SOSIP, which mimics the native trimer. The activity of anti-gp41 MAbs was superior in targeting monomeric gp41 but was comparable to that seen against trimers, which may not adequately expose gp41 epitopes. While anti-envelope MAbs in general mediated ADCP activity, anti-V2 MAbs displayed some dominance compared to other MAbs. Our demonstration that anti-V2 MAbs mediate ADCP activity suggests a functional mechanism for their contribution to protective efficacy.
Role of the PB2 627 Domain in Influenza A Virus Polymerase Function
Authors: Nilsson Benjamin E. , te Velthuis Aartjan J. W. , Fodor Ervin 
Published: January 2017

ABSTRACT

The RNA genome of influenza A viruses is transcribed and replicated by the viral RNA-dependent RNA polymerase, composed of the subunits PA, PB1, and PB2. High-resolution structural data revealed that the polymerase assembles into a central polymerase core and several auxiliary highly flexible, protruding domains. The auxiliary PB2 cap-binding and the PA endonuclease domains are both involved in cap snatching, but the role of the auxiliary PB2 627 domain, implicated in host range restriction of influenza A viruses, is still poorly understood. In this study, we used structure-guided truncations of the PB2 subunit to show that a PB2 subunit lacking the 627 domain accumulates in the cell nucleus and assembles into a heterotrimeric polymerase with PB1 and PA. Furthermore, we showed that a recombinant viral polymerase lacking the PB2 627 domain is able to carry out cap snatching, cap-dependent transcription initiation, and cap-independent ApG dinucleotide extension
in vitro
, indicating that the PB2 627 domain of the influenza virus RNA polymerase is not involved in core catalytic functions of the polymerase. However, in a cellular context, the 627 domain is essential for both transcription and replication. In particular, we showed that the PB2 627 domain is essential for the accumulation of the cRNA replicative intermediate in infected cells. Together, these results further our understanding of the role of the PB2 627 domain in transcription and replication of the influenza virus RNA genome.

IMPORTANCE
Influenza A viruses are a major global health threat, not only causing disease in both humans and birds but also placing significant strains on economies worldwide. Avian influenza A virus polymerases typically do not function efficiently in mammalian hosts and require adaptive mutations to restore polymerase activity. These adaptations include mutations in the 627 domain of the PB2 subunit of the viral polymerase, but it still remains to be established how these mutations enable host adaptation on a molecular level. In this report, we characterize the role of the 627 domain in polymerase function and offer insights into the replication mechanism of influenza A viruses.
Innate Immune Responses of Bat and Human Cells to Filoviruses: Commonalities and Distinctions
Authors: Kuzmin Ivan V. , Schwarz Toni M. , Ilinykh Philipp A. , Jordan Ingo , Ksiazek Thomas G. , Sachidanandam Ravi , Basler Christopher F. , Bukreyev Alexander 
Published: January 2017

ABSTRACTMarburg (MARV) and Ebola (EBOV) viruses are zoonotic pathogens that cause severe hemorrhagic fever in humans. The natural reservoir of MARV is the Egyptian rousette bat (Rousettus aegyptiacus); that of EBOV is unknown but believed to be another bat species. The Egyptian rousette develops subclinical productive infection with MARV but is refractory to EBOV. Interaction of filoviruses with hosts is greatly affected by the viral interferon (IFN)-inhibiting domains (IID). Our study was aimed at characterization of innate immune responses to filoviruses and the role of filovirus IID in bat and human cells. The study demonstrated that EBOV and MARV replicate to similar levels in all tested cell lines, indicating that permissiveness for EBOV at cell and organism levels do not necessarily correlate. Filoviruses, particularly MARV, induced a potent innate immune response in rousette cells, which was generally stronger than that in human cells. Both EBOV VP35 and VP24 IID were found to suppress the innate immune response in rousette cells, but only VP35 IID appeared to promote virus replication. Along with IFN-α and IFN-β, IFN-γ was demonstrated to control filovirus infection in bat cells but not in human cells, suggesting host species specificity of the antiviral effect. The antiviral effects of bat IFNs appeared not to correlate with induction of IFN-stimulated genes 54 and 56, which were detected in human cells ectopically expressing bat IFN-α and IFN-β. As bat IFN-γ induced the type I IFN pathway, its antiviral effect is likely to be partially induced via cross talk.IMPORTANCEBats serve as reservoirs for multiple emerging viruses, including filoviruses, henipaviruses, lyssaviruses, and zoonotic coronaviruses. Although there is no evidence for symptomatic disease caused by either Marburg or Ebola viruses in bats, spillover of these viruses into human populations causes deadly outbreaks. The reason for the lack of symptomatic disease in bats infected with filoviruses remains unknown. The outcome of a virus-host interaction depends on the ability of the host immune system to suppress viral replication and the ability of a virus to counteract the host defenses. Our study is a comparative analysis of the host innate immune response to either MARV or EBOV infection in bat and human cells and the role of viral interferon-inhibiting domains in the host innate immune responses. The data are useful for understanding the interactions of filoviruses with natural and accidental hosts and for identification of factors that influence filovirus evolution.
Prokaryotic Heme Biosynthesis: Multiple Pathways to a Common Essential Product
Authors: Dailey Harry A. , Dailey Tamara A. , Gerdes Svetlana , Jahn Dieter , Jahn Martina , O'Brian Mark R. , Warren Martin J. 
Published: January 2017

SUMMARY

The advent of heme during evolution allowed organisms possessing this compound to safely and efficiently carry out a variety of chemical reactions that otherwise were difficult or impossible. While it was long assumed that a single heme biosynthetic pathway existed in nature, over the past decade, it has become clear that there are three distinct pathways among prokaryotes, although all three pathways utilize a common initial core of three enzymes to produce the intermediate uroporphyrinogen III. The most ancient pathway and the only one found in the
Archaea
converts siroheme to protoheme via an oxygen-independent four-enzyme-step process. Bacteria utilize the initial core pathway but then add one additional common step to produce coproporphyrinogen III. Following this step, Gram-positive organisms oxidize coproporphyrinogen III to coproporphyrin III, insert iron to make coproheme, and finally decarboxylate coproheme to protoheme, whereas Gram-negative bacteria first decarboxylate coproporphyrinogen III to protoporphyrinogen IX and then oxidize this to protoporphyrin IX prior to metal insertion to make protoheme. In order to adapt to oxygen-deficient conditions, two steps in the bacterial pathways have multiple forms to accommodate oxidative reactions in an anaerobic environment. The regulation of these pathways reflects the diversity of bacterial metabolism. This diversity, along with the late recognition that three pathways exist, has significantly slowed advances in this field such that no single organism's heme synthesis pathway regulation is currently completely characterized.
Qualitative study of primary care clinicians’ views on point-of-care testing for C-reactive protein for acute respiratory tract infections in family medicine
Authors: Hardy Victoria , Thompson Matthew , Keppel Gina A , Alto William , Dirac M Ashworth , Neher Jon , Sanford Christopher , Hornecker Jaime , Cole Allison 
Published: January 2017

ObjectiveTo explore clinicians views of the barriers and facilitators to use of C-reactive protein (CRP) point-of-care tests (POCT) in US family medicine clinics for the management of acute respiratory tract infections (ARTIs) in adults.SettingFive family medicine clinics across two US states.Participants30 clinicians including 18 physicians, 9 physician residents, 2 physician assistants and 1 nurse practitioner, took part in the study.DesignA qualitative study using a grounded theory approach to thematically analyse focus group interviews.ResultsThese clinicians had limited access to diagnostic tests for patients with ARTI, and very little knowledge of CRP POCT. Three major themes were identified and included the potential clinical role of CRP POCT, concerns related to implementing CRP POCT and evidence needed prior to wider adoption in family medicine. Clinicians believed CRP POCT could support decision-making for some presentations of ARTIs and patient populations when used in conjunction with clinical criteria. Clinicians had concerns about possible overuse and inaccuracy of CRP POCT which they believed might increase antibiotic prescribing rates. Other concerns identified included integration of the test with clinic workflows and cost-effectiveness.ConclusionsClinicians stand at the forefront of antibiotic stewardship efforts, but have few diagnostic tests to help them confidently manage ARTIs. CRP POCT may facilitate some aspects of clinical practice. Incorporating CRP POCT with clinical guidelines may strengthen utility of this test, when there is diagnostic uncertainty.
Risk of disseminated intravascular coagulation in patients with type 2 diabetes mellitus: retrospective cohort study
Authors: Nogami Kenichiro , Muraki Isao , Imano Hironori , Iso Hiroyasu 
Published: January 2017

ObjectivesTo determine quantitatively the association between type 2 diabetes mellitus (T2DM) and disseminated intravascular coagulation (DIC).DesignRetrospective cohort study using a claims database.SettingMedical care institutions representing 9% of all secondary hospitals (acute care hospitals) in Japan.ParticipantsIn total, 797 324 admissions, comprising 435 354 patients aged 18–79 years at the time of admission, were enrolled between January 2010 and September 2014. All patients were diagnosed with diabetes or admitted to hospitals that provided laboratory data.Main outcome measuresIncidence of DIC reported by physicians in claims data.ResultsLogistic regression analysis found that the risk of DIC was significantly higher in T2DM patients than in non-DM patients (fully adjusted OR: 1.39 (95% CI 1.32 to 1.45)), independent of age, sex, admission year and potential underlying diseases. The higher risk of DIC in T2DM patients was apparent in those who were treated with insulin within the 30-day period prior to admission (1.53 (1.37 to 1.72)). When stratified by the potential underlying diseases, the risk of DIC was higher in T2DM patients with non-septic severe infection (1.67 (1.41 to 1.97)) and with solid tumour (1.59 (1.47 to 1.72)) than in non-DM patients with those underlying diseases. The risk was similar between T2DM and non-DM patients with sepsis (0.98 (0.90 to 1.08)) and lower in T2DM patients with acute leukaemia (0.70 (0.59 to 0.84)).ConclusionsT2DM was associated with a higher risk of DIC, particularly when recently treated with insulin, as well as among admissions with solid tumour or non-septic severe infection.