bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Roche and Abbott Cytomegalovirus Quantitative PCR Assays in Allogeneic Hematopoetic Cell Transplant Recipients
Authors: Mckinnon John , Janakiraman Nalini , Samuel Linoj , Lucic Danijela , Ramesh Mayur , Abreu-Lanfranco Odaliz , Farhan Shata , Osborn Zachary , Zhou Junying , Williams Katrina , Alangaden George 
Published: October 2017

Abstract

Background
Human Cytomegalovirus (CMV) infection is prevalent in patients undergoing transplantion (Tx) and carries significant morbidity and mortality. Quantification of CMV viremia has improved with the use of standardized international units and new commercial real time PCR assays. This study compares the current Roche cobas AmpliPrep/cobas TaqMan CMV test (TM assay) and Abbott Molecular RealTime CMV Investigational Use Only assay (ART assay) for quantification of CMV viremia in patients receiving allogeneic hematopoietic stem cell transplants (aHSCT).

Methods
Prospective CMV positive patients, planned for aHSCT, were consented prior to Tx and followed weekly up 12 weeks post-transplant (PT) and once ~3 months PT. Matched paired plasma samples were processed and analyzed per manufacturer instructions, Henry Ford clinical laboratory processed the samples using the TM assay and the McKinnon Research Laboratory processed the paired samples using the ART assay. Parametric and non-parametric analyses were conducted as appropriate.

Results
Fourteen patients enrolled, 1 patient withdrew after entering, 1 patient died after 9 weeks PT (primary disease). Patients received peripheral blood stem cells and 84.6% received myeloablative chemotherapy. In paired samples, quantifiable CMV by TM and ART assays was detected in 6 (5 treated) vs. 8 of 13 patients respectively. ART assay detected CMV in all patients with positive paired samples, 1 detected in an unpaired sample and in 2 patients missed by TM assay (P = 0.021). Assays also differed in samples with no detection, detectable and quantifiable CMV viremia, with more frequent detection in the ART assay (P = 0.009). Time to quantifiable viremia PT by TM and ART assays was a median of 5 vs. 3 weeks (P = 0.026). Bland-Altman plot shows higher viremia levels quantified using the ART assay (P = 0.023). After week 4 PT, ART assay results inversely correlated with platelets counts (P = 0.013). CMV viremia tended to persist 1.9 weeks longer using ART vs.. TM assay (P = 0.07).

Conclusion
CMV viremia was quantified earlier, at higher levels and persisted in patients with aHSCT using the ART assay compared with the TM assay. Further study is warranted to determine clinical impact of ART assay on the management of CMV viremia.

Disclosures
J. Mckinnon, Abbott Molecular: Speaker’s Bureau, Grant recipient and Speaker honorarium D. Lucic, Abbott Molecular: Employee, Salary
Optimization of a Polymerase Chain Reaction System for Whole Genome Amplification of Human Immunodeficiency Virus Type 2 (HIV-2)
Authors: Pappoe-Ashong Prince Jonathan , Sagoe Kwamena 
Published: October 2017

Abstract

Background
In this study, attempts were made to amplify the whole genome of HIV-2 using polymerase chain reaction (PCR) from viral RNA and proviral DNA extracted from archived human plasma and whole blood, respectively. The aim this study is to develop a PCR system that can be used to amplify the entire genome of all known subtypes and recombinant forms of HIV-2

Methods
Proviral DNA and viral RNA were extracted from archived human whole blood and plasma using Zymo Research Viral DNA kit and Zymo Research Viral nucleic acids kit, respectively. Primers that target the conserved sites of the 3’ and 5’ long terminal repeat were selected based on in silico analysis using Snapgene® tool version 2.1.0. Eight overlapping Primers for PCR whole genome amplification of HIV-2 were also selected and used for overlap PCR amplification of whole genome of HIV-2. Long range and overlapping PCR of whole genome of HIV-2 were carried out using long range Kit (New England Biolabs Inc., Ipswich, MA, USA) and cDNA synthesized using NEB ProtoScript II for proviral DNA and viral RNA templates. Amplified whole genome of HIV-2 was gel purified and PCR confirmed using two sets of primers ENVF/ENVG and EB2/EB5 and gel electrophoresis.

Results
Proviral DNA and viral RNA were successfully extracted from archived whole blood and plasma. Six primers were selected out of the 68 primer sequences retrieved using in silico analysis for long range single PCR amplification of HIV-2 whole genome. Primers P1/P8 and HIV2upA/HIV2lowA were successfully used in the whole genome amplification of HIV-2. Overlapping primers P1/P4, P6/P8, PolF/EnvG and Pol4F/EnvG covering the entire genome of HIV-2 were also successfully used in the whole genome amplification of HIV-2. The amplified whole genome fragment was confirmed to be HIV-2 by PCR using primers EB2/EB5 and EnvF/EnvG.

Conclusion
The techniques of long-range and overlapping amplification of HIV-2 whole genome may be useful in HIV-2 genotyping using viral RNA and proviral DNA. This study has led to the selection and shown novel primer combinations of already existing primers which can be used to amplify the entire genome of HIV-2.

Disclosures
All authors: No reported disclosures.
Comparison of Roche TaqMan v.2.0, Abbott RealTime and Modified Abbott Residual Viremia Assays in Testing of Routine Samples for Viremia Monitoring in HIV Care
Authors: Mckinnon John , Osborn Zachary , Taylor Tom , Zhou Jun Ying , Lucic Danijela , Clark Katelyn , Williams Katrina , Samuel Linoj 
Published: October 2017

Abstract

Background
Routine HIV RNA clinical monitoring frequently reports virermia (VL) as detectable, quantifiable &lt;50 or blips &gt;50 c/mL. To assess whether the results represent true increases or just assay variability, we designed comparisons of the Roche COBAS AmpliPrep / COBAS TaqMan HIV-1 Test version 2.0 (TM) and the Abbott RealTime HIV-1 assay (RT) to a residual viremia (RV) assay with a limit of detection of 3 c/mL, the Modified Abbott Residual Viremia assay (MARV).

Methods
HIV suppressed patients on stable therapy presenting for routine visits at the HIV clinic in Henry Ford Hospital (HFH) were prospectively enrolled. Blood samples and questionnaires were obtained at each visit. Paired plasma samples were processed and analyzed per manufacturer instructions; HFH clinical laboratory processed the samples using the TM assay and the McKinnon Research Laboratory performed the FDA approved RT assay and RV testing using the MARV assay. Parametric and non-parametric analyses were conducted as indicated.

Results
124 HIV patients are reported with a mean age of 51, mostly male (84%) and African American (64%). Mean CD4 cell counts were 661 cells/mm3. TM assay results for 196 plasma samples were not detectable (ND) 119 (61%), detectable (DT) 61 (31%) and quantifiable viremia (QV) &gt;20 c/mL 16 (8%). 5 patients had QV over 50 c/mL. 60 tested patients (49.5%) had at least one sample either DT or QV. TM results were not correlated to CD4 cell counts, antiretrovirals, medical conditions or reported adherence (avg. 97%). 174 RT and 187 MARV paired tests were ND on 142 (81%) / 121 (65%), DT on 34 (17%) RT, and quantifiable in 0% / 34 (33%) of the samples respectively. Higher VL detection by the TM was shown compared with the RT (P = 0.005) and MARV (P &lt; 0.001) assays. Mean QV by the MARV was 5.0 vs.. 55 c/mL on the TM assay (P &lt; 0.001). VL for all assays trends correlated when compared for ND, DT and &gt;20 copies/mL (P &lt; 0.001). Bland-Altman plots show higher VL detected by TM as compared with MARV (P &lt; 0.001) and good correlation between RT and MARV assays (P = 0.6).

Conclusion
HIV viremia is more frequently reported by TM assay as compared with the RT assay and was significantly higher than VL detected by the MARV assay. Over detection of VL by the TM assay may impact clinical decision making and increase cost of care.

Disclosures
J. Mckinnon, Abbott Molecular: Speaker’s Bureau, Grant recipient, Research grant and Speaker honorarium D. Lucic, Abbott Molecular: Employee, Salary
Experience of Sublingual Microcirculation Evaluation in Adults Patients with Severe Dengue
Authors: Rosso Fernando , Ospina Gustavo , Quiñones Edgardo , Sanz Ana Maria 
Published: October 2017

Abstract

Background
Severe microcirculatory changes are involved in the pathophysiological mechanisms that lead to irreversible final stages of dengue shock. We report our experience of the evaluation of sublingual microcirculation in adult patients with severe dengue

Methods
Adults patients with severe dengue (by WHO 2009 criteria) were included. Dengue diagnostics was made by positive serology for IgM / IgG, antigen NS1 or PCR. Sublingual Microcirculation (SM) was evaluated by Sidestream Dark Field imaging. Microvascular flow index (MFI), proportion of small-perfused vessels (%SVP), heterogeneity index (HI) and Total Vascular Density were calculated. All patients received Fluids Challenge (FC) at hospital admission.

Results
SM was assessed in 10 patients. The median age was 65 years [IQR: 34–70], 60% were male. Eight patients were admitted to the ICU, of which 63% required invasive ventilatory and vasoactive support. One patient died. After the fluid challenge, the median of the %SVP was 94 [IR: 97 – 77], the median of the MFI was 2.82 [IR: 2, 85 – 2, 14]. There were not significant differences in %SVP and MFI among the patients who survived. In the deceased patient, the %SVP with continuous flow was 59, 18% and the MFI was 1, 45; these values were significantly decreased compared with patients who survived. A significant negative correlation between hematocrit and %SVP, and MFI was found.

Conclusion
Initial fluid challenge, that identifies and treats volume depletion, could correct microcirculation abnormalities evaluated by SDF imaging. However, in the patient who did not respond to this challenge, significant alterations of the MFI and the %SVP were evidenced. There is a need for more studies to improve our understanding of the role of microcirculation evaluation in these patients.

Disclosures
All authors: No reported disclosures.
Clinically Important Resistance among Salmonella enterica Serotype Typhi Isolates—United States, 2003–2015
Authors: Medalla Felicita , Watkins Louise Francois , Chatham-Stephens Kevin , Reynolds Jared , Bicknese Amelia , Friedman Cindy 
Published: October 2017

Abstract

Background
Salmonella Typhi (Typhi) causes typhoid fever, accounting for an estimated 5,700 illnesses and 623 hospitalizations per year in the United States. Most infections are acquired during travel to regions outside the United States where typhoid fever is prevalent and antimicrobial resistance is a problem. Fluoroquinolones (e.g., ciprofloxacin) are considered the treatment of choice for susceptible Typhi infections due to their superior ability to concentrate intracellularly and in bile, however, nonsusceptibility has been associated with treatment failure or delayed response. Azithromycin and ceftriaxone are treatment options. We describe antimicrobial susceptibility among Typhi isolates in the United States and the implications for management.

Methods
The National Antimicrobial Resistance Monitoring System at CDC conducts susceptibility testing on all Typhi isolates submitted by public health laboratories. We used broth microdilution to determine minimum inhibitory concentrations (MICs) to agents representing 9 antimicrobial classes and categorized isolates according to criteria from the Clinical and Laboratory Standards Institute. We defined ciprofloxacin nonsusceptibility as MIC ≥0.12 μg/mL, ciprofloxacin resistance as MIC ≥1, azithromycin resistance as MIC ≥32, and ceftriaxone resistance as MIC ≥4.

Results
From 2003–2015, isolates were tested from 4,550 patients; 2,760 (61%) were ciprofloxacin nonsusceptible, 4% were ciprofloxacin resistant. One isolate was azithromycin resistant and none were ceftriaxone resistant. Ciprofloxacin nonsusceptibility increased from 39% in 2003 to 66% in 2015; resistance increased from 0.3% to 8%. Median age of patients was 23 years (range 1–99 years), 53% were male, most were from the Northeast (33%) or the West (29%), and 74% had an isolate from blood.

Conclusion
Two thirds of Typhi isolates exhibited ciprofloxacin nonsusceptibility, which has increased over the last decade, and full resistance is increasing. Clinicians should be aware of high rates of fluoroquinolone nonsusceptibility when selecting empiric therapy and should tailor antimicrobial treatment to susceptibility results when feasible. Azithromycin and ceftriaxone remain important treatment options.

Disclosures
All authors: No reported disclosures.
Broad In Vitro Activity Analysis of Tedizolid Compared with Other Agents against a Global Collection of Gram-Positive Isolates Causing Bloodstream Infections (2014–2016)
Authors: Mendes Rodrigo E , Shortridge Dee , Sader Helio S , Duncan Leonard R , Flamm Robert K 
Published: October 2017

Abstract

Background
Tedizolid (TZD) is an oxazolidinone derivative with oral and intravenous formulations approved for the treatment of acute bacterial skin and skin structure infections in the US, European countries, and other regions. This study evaluated TZD’s and comparators’ activity against a collection of clinical isolates causing bloodstream infections (BSI).

Methods
A total of 7,284 gram-positive isolates collected during the Surveillance of Tedizolid Activity and Resistance (STAR) Program for 2014–2016 were included. Bacteria were identified by standard algorithms and MALDI-TOF-MS. Susceptibility (S) testing was performed by CLSI methods, and interpretation used CLSI and EUCAST criteria.

Results
This Staphylococcus aureus collection contained 33.8% methicillin-resistant isolates. TZD was the most potent agent tested against all S. aureus (MIC50/90, 0.12/0.12 µg/mL; 100.0%S) and the MRSA subset (Table). Other tested agents described in Table also had in vitro MRSA coverage. 15.6% of enterococci were vancomycin-resistant, which were mostly Enterococcus faecium (59.8%). Linezolid (LZD), ampicillin, daptomycin (DAP), and vancomycin (VAN) showed equivalent MIC50 values (1 µg/mL) against E. faecalis, but these MIC50 results were 8-fold higher than TZD (MIC50, 0.12 µg/mL). Although LZD and DAP were highly active (98.9–99.4%S) against E. faecium, TZD MICs were 8- to 16-fold lower that LZD and DAP. Ceftaroline (CPT) showed the lowest MIC values against Streptococcus pneumoniae, whereas TZD and VAN were similarly active. TZD and CPT showed the lowest MIC90 values against viridans group streptococci, while CPT, ceftriaxone, and penicillin had the lowest MIC90 results against β-hemolytic streptococci.

Conclusion
TZD had potent activities against this global population of gram-positive clinical isolates that caused BSI. This in vitro potency and a favorable pharmacodynamic profile may suggest TZD is a promising candidate for treating BSI caused by gram-positive isolates, especially E. faecium.

Disclosures
R. E. Mendes, Merck: Research Contractor, Research grant; D. Shortridge, Merck: Research Contractor, Research grant; H. S. Sader, Merck: Research Contractor, Research grant; L. R. Duncan, Merck: Research Contractor, Research grant; R. K. Flamm, Merck: Research Contractor, Research grant
Lysin CF-301 Demonstrates In Vitro Synergy with Conventional Antibiotics against Staphylococcus aureus
Authors: Sauve Karen , Jandourek Alena , Cassino Cara , Schuch Raymond 
Published: October 2017

Abstract

Background
CF-301 is a novel, recombinantly-produced bacteriophage-derived lysin (cell wall hydrolase) and is the first agent of this class to enter clinical development in the US for the treatment of bacteremia including endocarditis due to S.aureus. This study evaluated the in vitro activity of CF-301 combined with each of 7 antistaphylococcal antibiotics including those considered to be current standard of care treatments for S.aureus bacteremia (daptomycin, vancomycin, oxacillin, nafcillin, and cefazolin) as well as linezolid and telavancin.

Methods
MICs for CF-301 were determined using a new AST medium for broth microdilution recently endorsed by the CLSI for use with CF-301. The testing medium consisted of cation-adjusted MHB supplemented with 25% horse serum and 0.5 mM DTT. Synergy was determined by checkerboard microdilution using the fractional inhibitory concentration index (FICI) for each combination in triplicate. For each antibiotic tested, an FIC mean was derived from each set of checkerboards by averaging 3 consecutive FIC values along the growth/no growth interface for each plate. Thus, 9 values were, used to generate the final mean. Synergy was defined as an FICI of ≤0.5; indifference was &gt;0.5 to &lt;2; and antagonism was ≥2. Each combination was examined against 10 MSSA and 10 MRSA strains.

Results
CF-301 synergized with daptomycin and vancomycin against each MSSA and MRSA strain, with FICI values between 0.254 and 0.5. Synergy was similarly observed against all 20 strains tested with oxacillin and nafcillin (FICI = 0.25–0.5); for the third β-lactam, cefazolin, synergy was observed with 17 strains (FICI = 0.75, for the remaining 3 strains). CF-301 synergized with televancin against 70% of the strains (FICI = 0.375–0.5), and was indifferent with the remainder (FICI = 0.625–1). CF-301 synergized with linezolid against 55% of the strains (FICI = 0.375–0.5), and was indifferent with the remainder (FICI = 0.625–0.75).

Conclusion
The broadly synergistic activity of CF-301 with conventional antistaphylococcal antibiotics against MSSA and MRSA suggests that CF-301 may afford therapeutic benefit by potentiating the activity antibiotics to treat serious infections for which there is an unmet medical need to improve outcomes.

Disclosures
K. Sauve, ContraFect Corp: Employee, Salary; A. Jandourek, ContraFect Corp: Employee, Salary; C. Cassino, ContraFect Corp: Employee, Salary; R. Schuch, ContraFect Corp: Employee, Salary
Synergistic Antiviral Activity of S-033188/S-033447, a Novel Inhibitor of Influenza Virus Cap-Dependent Endonuclease, in Combination with Neuraminidase Inhibitors In Vitro
Authors: Kitano Mitsutaka , Yamamoto Atsuko , Noshi Takeshi , Kawai Makoto , Yoshida Ryu , Sato Akihiko , Shishido Takao , Naito Akira 
Published: October 2017

Abstract

Background
S-033447, an active form of orally available prodrug S-033188, is a novel small molecule inhibitor of cap-dependent endonuclease that is essential for influenza virus transcription and replication. In this study, we evaluated the inhibitory effect of S-033188 in combination with neuraminidase inhibitors on the replication of influenza A/H1N1 virus in cultured cells.

Methods
The inhibitory effects of S-033447 in combination with NA inhibitors on the cytopathic effect of A/PR/8/34 strain in Madin–Darby canine kidney cells cultured for 2 days were tested and EC50 were determined. The combination index (CI), which were obtained when S-033188 and NA inhibitor were added at the closest ratio of each EC50 value, were used for the evaluation of these combinational effects (Table 1). CI values were calculated by the Chou and Talalay method, in which combinational effect were determined according to the criteria as follows: synergistic if CI ≤ 0.8, additive if 0.8 &lt; CI &lt; 1.2, and antagonistic if CI ≥ 1.2.
CI = (DA/A + B)/DA + (DB/A + B)/DB + (DA/A + B × DB/A + B)/(DA × DB)
DA: the EC50 of S-033447
DB: the EC50 of NA inhibitor
DA/A + B: the concentration of S-033447 giving 50% inhibition in combination with NA inhibitor at the closest ratio of each EC50 value
DB/A + B: the concentration of NA inhibitor giving 50% inhibition in combination with S-033447 at the closest ratio of each EC50 value

Results
All CI values were lower than 0.8, under the condition that both S-033447 and NA inhibitor (oseltamivir acid, zanamivir hydrate, laninamivir, or peramivir trihydrate) were added at the closest ratio of each EC50 value (Table 1).

Conclusion
S-033447 in combination with oseltamivir acid, zanamivir hydrate, laninamivir, or peramivir trihydrate synergistically inhibited the replication of influenza A/H1N1 virus in MDCK cells.

Disclosures
All authors: No reported disclosures.
In Vitro Activity of Ceftolozane-Tazobactam vs. Antimicrobial Non-Susceptible Pseudomonas aeruginosa Clinical Isolates Obtained from Across Canada as Part of the CANWARD Study, 2008–2016
Authors: Walkty Andrew , Adam Heather J , Baxter Melanie , Lagace-Wiens Philippe , Karlowsky James , Hoban Daryl , Zhanel George 
Published: October 2017

Abstract

Background
Ceftolozane-tazobactam (C/T) is a novel β-lactam β-lactamase inhibitor combination with a broad spectrum of activity that includes Pseudomonas aeruginosa. The purpose of this study was to evaluate the in vitro activity of C/T and relevant comparators vs. a large collection of antimicrobial non-susceptible (NS) P. aeruginosa clinical isolates obtained from patients across Canada (CANWARD, 2008–2016).

Methods
From January 2008 to December 2016, inclusive, 12 to 15 sentinel hospitals across Canada submitted clinical isolates from patients attending ERs, medical and surgical wards, hospital clinics, and ICUs (CANWARD). Each center was asked to annually submit clinical isolates (consecutive, one per patient/infection site) from blood, respiratory, urine, and wound infections. Susceptibility testing was performed using broth microdilution as described by CLSI. Multidrug-resistant (MDR) P. aeruginosa were defined as isolates that tested NS to at least one antimicrobial from ≥3 classes. Extensively drug-resistant (XDR) P. aeruginosa were defined as isolates that tested NS to at least one antimicrobial from ≥5 classes.

Results
3229 P. aeruginosa isolates were obtained as a part of CANWARD. The in vitro activity of C/T and relevant comparators is presented below.

Conclusion
C/T demonstrated excellent in vitro activity vs. antimicrobial NS P. aeruginosa clinical isolates, including MDR, XDR, and meropenem NS subsets. It may prove useful in the treatment of infections caused by these organisms.

Disclosures
D. Hoban, Abbott: Research relationship, Research support Achaogen: Research relationship, Research support Astellas: Research relationship, Research support Merck Canada: Research relationship, Research support Merck USA: Research relationship, Research support Paratek Pharma: Research relationship, Research support Pharmascience: Research relationship, Research support Sunovion: Research relationship, Research support Tetraphase: Research relationship, Research support The Medicines Co.: Research relationship, Research support Zoetis: Research relationship, Research support; G. Zhanel, Achaogen: Research relationship, Research support Astellas: Research relationship, Research support Merck Canada: Research relationship, Research support Merck USA: Research relationship, Research support Paratek Pharma: Research relationship, Research support Pharmascience: Research relationship, Research support Sunovion: Research relationship, Research support Tetraphase: Research relationship, Research support The Medicines Co.: Research relationship, Research support Zoetis: Research relationship, Research support