bluuebunny/crossref_metadata_2025_split huggingface dataset:
2144. Performance of 2019 CLSI Ciprofloxacin Breakpoint Antimicrobial Susceptibility Testing Algorithms for Enterobacteriaceae and Pseudomonas aeruginosa Directly from Positive Blood Culture on the Accelerate Pheno™ System
Authors: Shamsheyeva Alena , Oppermann Niels , Taku Aimee , Ndobegang Anyangatia , Gamage Dulini , Chantell Christina , Humphries Romney 
Published: October 2019

Abstract

Background
The Clinical and Laboratory Standards Institute (CLSI) updated fluoroquinolone breakpoints in 2019 in response to evolving resistance and new outcome data. The performance of updated antimicrobial susceptibility testing (AST) algorithms for ciprofloxacin with the 2019 breakpoints for Enterobacteriaceae and Pseudomonas aeruginosa was evaluated using the Accelerate Pheno™ system with contrived positive blood culture samples compared with broth microdilution (BMD).

Methods
A total of 294 clinical isolates (100 P. aeruginosa, 82 Klebsiella spp., 56 E. coli, 24 Citrobacter spp., 14 Enterobacter spp., 15 Proteus spp., and 3 S. marcescens) were tested with ciprofloxacin. Aliquots of BD BACTEC™ Standard Aerobic media containing healthy donor blood were seeded with 10–100 bacterial cells and incubated until positivity. Aliquots of the positive blood cultures were run using the Accelerate PhenoTest™ BC kit on the Accelerate Pheno™ system according to the manufacturer instructions for use. Results were obtained using an updated ciprofloxacin algorithm and compared with CLSI standard reference BMD. Only samples with valid results with both the Accelerate Pheno™ system and reference BMD were included in analysis. Essential agreement (EA), categorical agreement (CA), very major error (VME), major error (ME) and minor error (mE) rates were calculated using 2019 CLSI breakpoints.

Results
EA and CA for all antimicrobial/organism combinations were >94%. There were 2 MEs (1 K. pneumoniae, 1 C. freundii) and no VMEs.

Conclusion
Results with the new research use only (RUO) algorithms are very good and meet FDA acceptance criteria for AST performance. These data will be submitted to the FDA for clearance, once FDA recognizes the CLSI breakpoints.

Disclosures
All authors: No reported disclosures.
2165. Helicobacter pylori Infections in the Bronx, New York: Whole-Genome Sequencing for Rapid Genotypic Susceptibility Testing
Authors: Rajagopalan Saranathan , Szymczak Wendy , Jacobs William , Behin Daniel , Pan Debra , Levi Michael 
Published: October 2019

Abstract

Background
Susceptibility-guided treatment of H. pylori is superior to empiric therapy. We determined the accuracy of whole-genome sequencing (WGS) compared with phenotypic testing using CLSI/EUCAST breakpoints.

Methods
Thirty-three clinical isolates of H. pylori cultured from gastric biopsies were sequenced with a coverage range between 40x and 80x using Illumina Miseq platform and the reads were assembled and annotated with PATRIC. Phenotypic susceptibility tests were performed using E-test strips under microaerophilic conditions for 72 hours. Mutations associated with amoxicillin, tetracycline, clarithromycin, levofloxacin, metronidazole and rifampin resistance were examined.

Results
Of the 33 isolates, two were phenotypically resistant to amoxicillin: one carried a β-lactamase gene (blaTEM-116) and the other exhibited a point mutation pbp2 (A541T). All isolates were tetracycline susceptible phenotypically, but three isolates had point mutations in 16S rRNA that are associated with resistance (A926G). Clarithromycin results showed a good correlation between methods. Nine clarithromycin-resistant isolates demonstrated point mutations in 23S rRNA (A2142G/A2143G). Fifteen isolates were phenotypically resistant to levofloxacin, but resistance mutations were found in only 14 strains (N87I/N87K/D91Y/D91N/D91G/D99N in gyrA). We analyzed our strains for the presence of intact genes rdxA and frxA, either of which convert the prodrug form of metronidazole into the active form. Twenty-four of 33 isolates were tested phenotypically. We found 3 isolates with truncations in both genes. These isolates had metronidazole MICs >256. The presence of one or both intact genes did not always result in low MICs, indicating that there may be significant point mutations that contribute to resistance. Rifampin was not tested phenotypically, but no mutations in rpoB were found. In summary, the correlation of WGS and phenotypic testing was 100% for amoxicillin and clarithromycin, 97% for levofloxacin, 91% for tetracycline (n = 33), and 67% for metronidazole (n = 24).

Conclusion
WGS provides a detailed analysis of H. pylori resistance and a broader analysis of antimicrobials that may be of clinical value. Additional studies are needed for genotypic prediction of metronidazole resistance.

Disclosures
All authors: No reported disclosures.
2166. Performance Study on the New ETEST® Piperacillin/Tazobactam (P/T) MIC Strip
Authors: Martelin Roland , Pillon Edwige , Cutivet Emilie , Pompilio Marion , Halimi Diane , Durand Geraldine 
Published: October 2019

Abstract

Background
Piperacillin/Tazobactam combination is a first-line antibiotic and carbapenem sparing option for severe infections due to Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter baumannii. ETEST® strips allow to determine antimicrobial Minimum Inhibitory Concentration (MIC). ETEST® Piperacillin/Tazobactam (Ptc) was developped in 1995 against agar dilution reference method. Since then, resistance to Piperacillin/Tazobactam has been increasing and broth microdilution (BMD) substituted for agar dilution as the reference method. The new ETEST® P/T strip for determining MIC of Enterobacteriaceae, P. aeruginosa and A. baumannii was developed against BMD using a panel of recent strains well genotypically characterized. The aim of this study was to compare the performance of both strips on a panel of challenging strains harboring different-resistant mechanisms.

Methods
A total of 64 strains were tested using ETEST® P/T, ETEST® PTc and BMD: 48 Enterobacteriaceae including 25 resistant strains and 16 P. aeruginosa including 11 resistant strains. The results were analyzed for essential (EA) and category (CA) agreements, minor (mE), major (ME) and very major (VME) error rates using FDA/CLSI 2019 breakpoints (Enterobacteriaceae, P. aeruginosa: ≤ 16/4(S); ≥ 128/4(R) µg/mL).

Results
Although the panel of strains was challenging including different resistant mechanisms (acquired penicillinase, high-level cephalosporinase, acquired cephalosporinase, ESBL, carbapenemase), the new ETEST® P/T performance was significantly improved for Enterobacteriaceae with an EA at 92,2% without ME or VME. This improvement was also linked to the easiest reading (significant decrease of microcolonies in the ellipse zone). For P. aeruginosa, the performance was similar between the two strips but the new ETEST® P/T was better correlated with the BMD and showed an EA of 100%. The results are summarized in the table.

Conclusion
The new ETEST® P/T improved the MIC determination and resistance detection, as well as the reading of MIC end points for the routine use. This study emphasizes the need to check the performance of the antimicrobial susceptibility testing products by testing strains reflecting the current epidemiology.

Disclosures
All authors: No reported disclosures.
2168. Comparison of Rapid Diagnostic Tests for Bloodstream Infections Using Desirability of Outcome Ranking Management of Antimicrobial Therapy (DOOR-MAT)
Authors: Claeys Kimberly C , Hopkins Teri , Kpadeh-Rogers Zegbeh , Jiang Yunyun , Evans Scott R , Johnson J Kristie , Leekha Surbhi 
Published: October 2019

Abstract

Background
Rapid diagnostic tests (RDTs) for bloodstream infection (BSIs) are increasingly common. Decisions regarding which RDT to implement remains a clinical challenge given the diversity of organisms and resistance mechanisms detected by different platforms. The desirability of Outcome Ranking Management of Antimicrobial Therapy (DOOR-MAT) has been proposed as a framework to compare RDT platforms but reports of clinical application are lacking. This study compared potential antibiotic decisions based on results of two different RDTs for BSI using DOOR-MAT.

Methods
Retrospective study at University of Maryland Medical Center from August 2018 to April 2019 comparing Verigene® BC (VBC) to GenMark Dx ePlex® BCID for clinical blood cultures. VBC was part of standard of care, ePlex was run on discarded fresh or frozen blood samples. In this theoretical analysis, RDT result and local susceptibility data were applied by two Infectious Diseases pharmacists to make decisions regarding antibiotic selection in a blinded manner. Cohen’s Kappa statistic summarized overall agreement. DOOR-MAT, a partial credit scoring system, was applied to decisions based on final organism/susceptibility results (Figure 1). Scores were averaged between reviewers and mean scores compared between RDT systems using the t-test. Additionally, a sensitivity analysis with varied point assignment among Gram-negatives (AmpC-producers) was conducted.

Results
110 clinical isolates were included; 41 Gram-negative, 69 Gram-positive organisms. Overall agreement was 82% for VBC and 83% for ePlex. The average score for VBC was 86.1 (SD 31.3) compared with ePlex 92.9 (SD 22.9), P = 0.004. Among Gram-negatives, the average score for VBC was 79.9 (SD 32.1) compared with ePlex 88.1 (SD 28.8), P = 0.032. Among GPs the average score for VBC was 89.9 (SD 30.4) compared with ePlex 95.8 (SD 18.3), P = 0.048. Sensitivity analysis demonstrated an average score for of 89.9 (SD 30.4) for VBC compared with 95.8 (SD 18.3) for ePlex, P = 0.27.

Conclusion
The use of a partial credit scoring system such as the DOOR-MAT allows for comparisons between RDT systems beyond sensitivity and specificity allowing for enhanced clinical interpretation. In this theoretical comparison, the Genmark ePlex BCID scored higher among both GP and GN organisms.

Disclosures
All authors: No reported disclosures.
2191. The Sputum FilmArray Pneumonia Panel (SFAPP) Outperforms a Diagnostic Bundle in Patients with Community-Acquired Pneumonia (CAP)
Authors: Gilbert David N , White Emma , Ferdosian Shirin , Gelfer Gita , Wang Lian , Leggett James 
Published: October 2019

Abstract

Background
This study compares the detection of respiratory pathogens between a multitest “Bundle” (MTB) and the Sputum FilmArray Pneumonia Panel (SFAPP).

Methods
Patients admitted from the ED with CAP were enrolled. The SFAPP probed for the presence of 18 bacterial species and 17 viral targets. The results were compared with pathogen detection with an MTB: (a) culture of sputum and blood; (b) urine antigens of S. pneumoniae and Legionella pneumophila; (c) Nasopharyngeal (NP) Respiratory FilmArray (NPRFA) panel which detects 17 viruses and 3 bacteria; and (d) nasal NAATs for S. pneumoniae and S. aureus. Two serum procalcitonin (PCT) levels helped separate bacterial colonization from invasion.

Results
Of 400 enrolled patients, 121 (30%) were non-evaluable due to a lack of a sputum specimen, 72 (18%) with a final diagnosis other than CAP, and other reasons in 21 (5%). Herein, the results of 186 (47%) evaluable patients with CAP and the Pneumonia Severity Index values of over 90 in 64.5%. The SFAPP detected viruses in 114/186 (61.3%) patients compared with 73/186 (39.2%) with the NPRFAP, p. The SFAPP detected bacterial pathogen(s) in 140/186 (75.3%) of patients vs. 117/183 (62.9%) with the MTB, pH. influenzae, M. catarrhalis, and S. agalactiae, p. A potential pathogenic bacteria and/or virus was detected in 176 of the 186 (95%) evaluable patients. Patients were classified as: virus detected (22); bacteria detected (57); bacteria and virus (97); CAP but no pathogen detected (10). The distribution of serum PCT levels by pathogen detected is shown in Figure 1. The dashed line is the 0.25 ng/mL “cut-off” to help separate colonization from invasion by bacteria. Antibiotic use was less in influenza patients with low PCT levels, p. In 22 patients with only virus detected and PCT.

Conclusion
The Sputum FilmArray Pneumonia Panel detected more bacteria and viral potential pathogens than the Multitest Bundle that included the Nasopharyngeal FilmArray Panel. The Sputum FilmArray Pneumonia Panel may allow removal of nasopharyngeal swabs and urine antigens from the MTB.

Disclosures
All authors: No reported disclosures.
2199. The Etiology of Community-Acquired Pneumonia with Attention to the Role of Normal Respiratory Flora
Authors: Musher Daniel M , Jesudasen Sirus , Barwatt Joseph W , Cohen Daniel N , Rodriguez-Barradas Maria C 
Published: October 2019

Abstract

Background
Intensive studies have failed to identify an etiologic agent in >50% of patients (patients) who are hospitalized for community-acquired pneumonia (CAP). Gram stain and culture of sputum samples frequently yield “normal respiratory flora” (NRF). We hypothesized that careful study might (1) increase the yield of recognized pathogens; and (2) show, in some patients, an etiologic role for NRF.

Methods
We studied a convenience sample of adults hospitalized for CAP at a VA Medical Center if they met four criteria: (1) clinical syndrome consistent with pneumonia; (2) newly recognized pulmonary infiltrate; (3) sputum with > 10 WBC per epithelial cell; and (4) < 18 hours antibiotic treatment. For quantification of bacteria, sputum was liquefied in 2% N-acetyl cysteine and diluted serially. Other studies in nearly all patients included blood cultures, urine for pneumococcal (Spn) and Legionella antigen, procalcitonin, B-natriuretic protein and PCR for 13 respiratory viruses, Mycoplasma and Chlamydia. >106 bacteria/mL and a consistent Gram stain indicated a bacterial cause, positive viral PCR indicated a viral cause, and both indicated coinfection.

Results
119 patients met study criteria. Recognized bacterial pathogens alone were identified in 47 (40%) cases led by Spn 17 (14%), Haemophilus 17 (14%) and S. aureus 6 (5%). A virus alone was identified in 17 (15%) and coinfection in 11 (9%). We applied these same criteria for NRF. NRF alone were found in 22 (19%) patients with S. mitis predominating. NRF and a respiratory virus were coinfecting in 10 (8%) patients. In total, with the inclusion of NRF, an etiologic agent was found in 95% of patients.

Conclusion
Our high yield is attributable to selection criteria. With a good-quality sputum and absent prolonged antibiotics, a bacterial cause for CAP was found in 59% of patients, a viral cause in 15%, and coinfection in 17%. Bacterial CAP due to recognized pathogen follows microaspiration of colonizing bacteria from the upper airways. Aspiration of a sufficient inoculum of so-called NRF, especially in older adults or those with damaged clearance mechanisms, might well do the same. Careful microbiologic study of patients who are able to provide a valid sputum sample before prolonged antibiotics enables a microbiologic diagnosis in nearly all cases and shows a potential etiologic role for NRF in about 20%.

Disclosures
All authors: No reported disclosures.
2234. Outcomes by Age and Gender from a Global Phase 3 Study of Delafloxacin (DLX) in Community-Acquired Bacterial Pneumonia (CABP)
Authors: Madej Andrzej , Pullman John , Popescu Monica , Quintas Megan , Lawrence Laura , Li Yang , Cammarata Sue 
Published: October 2019

Abstract

Background
Delafloxacin (DLX) is a fluoroquinolone, approved in the United States for treatment of ABSSSI. DLX has no preclinical signals for QT prolongation and has no QT prolongation in a validated challenge study. Risk of QT prolongation is a consideration in antibiotic selection for elderly hospitalized CABP patients. A Phase 3 CABP trial with DLX was analyzed with a focus on age and gender.

Methods
Data on age and gender were reviewed from a multicenter, randomized, double-blind trial of adults with CABP. Patients were randomized 1:1 to DLX or moxifloxacin (MOX) treatment for 5–10 days. Patients received a minimum of 3 days of IV treatment, then were switched to oral at MD discretion. A key clinical endpoint was the investigator-assessment at Test of Cure (TOC) 5–10 days after the end of treatment. Clinical success was defined as complete or near resolution of signs and symptoms and no further antibiotics needed

Results
In the overall study, 859 patients were randomized with a mean age of 60 years (55.5% <65, 44.5% ≥65, 21.2% ≥75; range 18–93); 58.7% were male; 25.4% and 1.4% were PORT class IV and V; 28.6% multi-lobar pneumonia. Table shows the comparison of DLX and MOX clinical response at TOC in the Intent to Treat (ITT) population. Overall, DLX was well tolerated, with similar related adverse events (AE) between treatment groups regardless of age (< 65: 16.7% DLX, 13.3% MOX; ≥ 65: 13.4% DLX, 11.7% MOX) or gender (male: 16.0% DLX, 11.1% MOX; female 14.0% DLX, 14.9% MOX). The most common treatment-related AEs for DLX were diarrhea and transaminase elevations which were mild-to-moderate and did not routinely lead to discontinuation. There were no reports of potential QT prolongation on DLX.

Conclusion
Based on age and gender, DLX had comparable outcomes to MOX in clinical success at TOC. DLX was also well tolerated regardless of age or gender. DLX may offer a promising alternative in the treatment of CABP including elderly patients.

Disclosures
All authors: No reported disclosures.
2236. Stool-Derived Inflammatory Mediators Serve as Biomarkers of Severity in Clostridium difficile Infection
Authors: Motyka Jonathan , Penkevich Aline , Perry D Alex , Weiner Shayna , Standke Alexandra , Keidan Micah , Young Vincent B , Rao Krishna 
Published: October 2019

Abstract

Background
Clostridium difficile infection (CDI) is a major public health concern and frequently results in severe disease, including death. Predicting subsequent complications early in the course can help optimize treatments and improve outcomes. However, models based on clinical criteria alone are not accurate and/or do not validate. We hypothesized that inflammatory mediators from the stool would be biomarkers for severity and complications.

Methods
Subjects were included after testing positive for toxigenic C. difficile by the clinical microbiology laboratory via enzyme immunoassay (EIA) for glutamate dehydrogenase and toxins A/B, with reflex to tcdB gene PCR for discordants. Stool was thawed on ice, diluted 1:1 with PBS and protease inhibitor, centrifuged, and the supernatant was analyzed by a custom antibody-linked bead array with 17 inflammatory mediators. Measurements were normalized and log-transformed. IDSA severity was defined by serum white blood cell count > 15000 cells/µL or creatinine 1.5-fold above baseline. Primary 30-day outcomes were all-cause mortality and attributable disease-related complications (DRC): ICU admission, colectomy, and/or death. Analyses included principal components, permutational multivariate ANOVA (PERMANOVA), and logistic regression ± L1 regularization and 5-fold cross validation. The area under the receiver operator characteristic curve (AuROC) was computed.

Results
We included 225 subjects, with 124 females (55.1%), average age 58.5 (±17), and more PCR+ than toxin EIA+ (170 vs. 55, respectively). IDSA severity, death, and DRCs occurred in 79 (35.1%), 14 (6.2%), and 12 (5.3%) subjects, respectively. PCA and PERMANOVA showed IDSA severity (P = 0.009) but not death or DRCs associated with the panel (figure). Several inflammatory mediators associated with IDSA severity and death (table). Machine learning models had AuROCs of 0.77 (IDSA severity), 0.84 (death), and 0.7 (DRCs).

Conclusion
We found that specific inflammatory mediators from the stool of patients with CDI associate with severity and complications. These results are promising, but need replication in a larger dataset and should be incorporated into models that include clinical covariates prior to deployment.

Disclosures
All authors: No reported disclosures.
2261. Oral Fosfomycin for Treatment of Urinary Tract Infections Due to Extended-Spectrum β-Lactamase and Carbapenem-Resistant Enterobacteriaceae
Authors: Hefler Jade L , Perez Katherine K , Musick William L 
Published: October 2019

Abstract

Background
Urinary tract infections (UTIs) caused by extended spectrum β-lactamase (ESBL) and carbapenem-resistant Enterobacteriaceae (CRE) pose a significant challenge due to limited treatment options. The objective of this study was to compare outcomes in patients treated with standard IV therapy or oral fosfomycin for ESBL and CRE UTIs.

Methods
Retrospective cohort review of inpatients diagnosed with ESBL and CRE UTIs between June 2016 and September 2017 at a seven-hospital system. Patients with polymicrobial UTI, bloodstream infections, additional anatomical site with ESBL/CRE, or those requiring renal replacement therapy were excluded. Only patients with documented fosfomycin susceptible isolates in vitro were included. Eligible patients were divided into two groups: standard IV therapy (SDTx) or fosfomycin therapy (FOS). FOS group could receive ≤72 hours of other active antibiotics from urine culture collection (UTI onset) to the first dose of fosfomycin. Quick sequential organ failure assessment (qSOFA) scores were calculated at UTI onset. The primary endpoint was functional cure defined as resolution of symptoms without microbiological failure. Microbiological failure was defined as a positive urine culture within the index hospitalization or 30 days.

Results
There were 70 patients included: 31 treated with SDTx and 39 with FOS. ESBL Echerichia coli was most common, accounting for 58% of UTIs in SDTx and 71.8% in FOS. ESBLs accounted for 71% (n = 22/31) of UTIs in SDTx and 89.7% (n = 35/39) in FOS. The overall qSOFA score was 0.7 (range, 0–3) with the majority of patients scoring < 2 (80.6% in SDTx vs. 92.3% in FOS; P = 0.29). There was no significant difference in functional cure rate (n = 30, 96.8% SDTx vs. n = 37, 94.9% FOS; P = 0.83). SDTx patients had a longer length of stay (15.3 days vs. 7.3 days with FOS; P = 0.04), duration of active therapy (7.6 days vs. 3 days with FOS; P < 0.0001), and time from UTI onset to discharge (10.3 days vs. 6.6 days with FOS; P = 0.002). There were no adverse drug events reported.

Conclusion
Oral fosfomycin was a safe and effective alternative to standard IV therapy for ESBL and CRE UTIs in this investigation and demonstrated similar functional cure rates. Additionally, patients treated with fosfomycin had shorter hospitalizations and durations of antibiotic therapy.

Disclosures
All authors: No reported disclosures.