Clinical Accuracy and Impact of Plasma Cell-Free DNA Fungal PCR Panel for Non-Invasive Diagnosis of Fungal Infection

BACKGROUND

Invasive fungal infection (IFI) is a growing cause of morbidity and mortality in oncology and transplant patients. Diagnosis of IFI is often delayed due to need for invasive biopsy and low sensitivity of conventional diagnostic methods. Fungal cell-free DNA (cfDNA) detection in plasma is a novel testing modality for the non-invasive diagnosis of IFI.

METHODS

A novel bioinformatic pipeline was created to interrogate fungal genomes and identify multicopy sequences for cfDNA PCR targeting. A real-time PCR panel was developed for 12 genera and species most commonly causing IFI. Sensitivity and specificity of the fungal PCR panel were determined using plasma samples from patients with IFI and non-IFI controls. Clinical impact of fungal PCR panel was evaluated prospectively based on the treating team's interpretation of the results.

RESULTS

Overall, the sensitivity and specificity were 56.5% (65/115, 95% confidence interval [CI], 47.4%-65.2%) and 99.5% (2064/2075; 95% CI, 99.0%-99.7%), respectively. In the subset of patients with an optimized plasma volume (2mL), sensitivity was 69.6% (48/69; 95% CI, 57.9%-79.2%). Sensitivity was 91.7% (11/12; 95% CI, 62.5%-100%) for detection of Mucorales agents, 56.3% (9/16; 95% CI, 33.2%-76.9%) for Aspergillus species, and 84.6% (11/13; 95% CI, 56.5%-96.9%) for Candida albicans. In a prospective evaluation of 226 patients with suspected IFI, cfDNA testing was positive in 47 (20.8%) patients and resulted in a positive impact on clinical management in 20/47 (42.6%).

CONCLUSIONS

The fungal cfDNA PCR panel offers a non-invasive approach to early diagnosis of IFI, providing actionable results for personalized care.

SARS-CoV-2 infection and COVID-19 severity in individuals with prior seasonal coronavirus infection

We show that individuals with documented history of seasonal coronavirus have a similar SARS-CoV-2 infection rate and COVID-19 severity as those with no prior history of seasonal coronavirus. Our findings suggest prior infection with seasonal coronavirus does not provide immunity to subsequent infection with SARS-CoV-2.

Reactivation of Chagas Disease in a Patient With an Autoimmune Rheumatic Disease: Case Report and Review of the Literature

Reactivation of Chagas disease has been described in immunosuppressed patients, but there is a paucity of literature describing reactivation in patients on immunosuppressive therapies for the treatment of autoimmune rheumatic diseases. We describe a case of Chagas disease reactivation in a woman taking azathioprine and prednisone for limited cutaneous systemic sclerosis (lcSSc). Reactivation manifested as indurated and erythematous cutaneous nodules. Sequencing of a skin biopsy specimen confirmed the diagnosis of Chagas disease. She was treated with benznidazole with clinical improvement in the cutaneous lesions. However, her clinical course was complicated and included disseminated CMV disease and subsequent septic shock due to bacteremia. Our case and review of the literature highlight that screening for Chagas disease should be strongly considered for patients who will undergo immunosuppression for treatment of autoimmune disease if epidemiologically indicated.

1489. Safety and Performance of a Pharmacist-Driven Nasal MRSA PCR Protocol for De-escalation of Empiric Vancomycin for Suspected Pneumonia at an Academic Medical Center

Background

Limited published data supports the de-escalation of empiric anti-methicillin resistant Staphylococcus aureus (MRSA) antibiotics for suspected pneumonia upon negative nasal MRSA screening. Besides limited sample sizes, special populations, such as those who are immunocompromised and/or critically ill, have been underrepresented in these reports. We describe real-world efficacy and safety of a pharmacist-driven nasal MRSA PCR testing protocol implemented at Stanford Health Care in May 2018 across a diverse patient population.

Methods

This was an observational cohort study of adult patients who received vancomycin for empiric pneumonia before (PRE) vs after (POST) implementation of a pharmacist-driven nasal MRSA PCR testing protocol (between 05/01/2017 - 08/31/2017 (PRE) and 5/7/2018 - 12/31/2019 (POST). The primary outcome measure was duration of vancomycin administration. Secondary outcomes included time to vancomycin discontinuation, frequency of restarting vancomycin for empiric pneumonia within 7 days, acute kidney injury (defined as “risk” by RIFLE criteria), and MRSA respiratory cultures. Statistical methods are described in Figure A.

Figure A. Statistical methods

Results

Total of 610 patients were included in this study with 116 in the PRE group and 494 in the POST group. Over 40% were critically ill and approximately 37% were immunocompromised in both groups (Table 1). For the primary outcome, median vancomycin duration was significantly shorter in the POST group (1.29 days; 95% CI 1.13-1.45) vs. PRE group (1.98 days; 95% CI 1.49-2.46) (p < 0.0005), a 34.8% reduction (Figure 1). Median vancomycin duration was lower in patients with a negative vs positive nasal MRSA PCR (1.20 days [95% CI 1.08-1.33] vs 2.53 days [95% CI 1.77-3.29], p < 0.0005), a 52.6% reduction (Figure 2). MRSA was recovered in respiratory cultures in 1.7% vs 1.4% in the PRE vs POST groups. One (0.002%) patient had a negative nasal MRSA PCR but culture-confirmed MRSA pneumonia and recovered after completing a treatment course. Secondary safety outcomes were similar between groups (Table 2).

Tables 1 and 2: Baseline Characteristics and Secondary Outcomes

Figure 1. Primary Outcome: Kaplan–Meier Estimates of Cumulative Active Vancomycin Therapy Before and After Implementation of Nasal MRSA PCR protocol

Figure 2. Secondary Outcome: Figure 2. Kaplan–Meier Estimates of Cumulative Active Vancomycin Therapy in Patients with Negative vs Positive Nasal MRSA PCR

Conclusion

Pharmacist-driven nasal MRSA PCR testing is effective and safe in early de-escalation of empiric vancomycin used for pneumonia treatment in a diverse population including critically ill and immunocompromised patients.

Disclosures

All Authors: No reported disclosures

Concurrent Trypanosoma cruzi and Cytomegalovirus Reactivation in an Immunosuppressed Patient With Limited Cutaneous Systemic Sclerosis

Chagas disease, a multisystem infection caused by the protozoan Trypanosoma cruzi, is primarily found in Latin America. In recent years, prevalence has increased in the United States, where reactivation is the most common clinical scenario. Here, we describe cutaneous reactivation of T. cruzi in a patient with limited cutaneous systemic sclerosis on immunosuppression therapy who simultaneously presented with cytomegalovirus reactivation. Histopathology showed parasitized histiocytes in the superficial and deep dermis. Occasional epidermal keratinocytes were also parasitized, and rare organisms were also seen in the walls of blood vessels. Also noted were viral cytopathic changes within the vascular endothelium, and immunostaining confirmed cytomegalovirus. In this report, we describe the difference in cutaneous findings between reactivated and acute Chagas disease, and we also review the histopathologic features that help distinguish T.cruzi from other intracellular organisms.

Plasmonic and Electrostatic Interactions Enable Uniformly Enhanced Liquid Bacterial Surface-Enhanced Raman Scattering (SERS)

Surface-enhanced Raman spectroscopy (SERS) is a promising cellular identification and drug susceptibility testing platform, provided it can be performed in a controlled liquid environment that maintains cell viability. We investigate bacterial liquid-SERS, studying plasmonic and electrostatic interactions between gold nanorods and bacteria that enable uniformly enhanced SERS. We synthesize five nanorod sizes with longitudinal plasmon resonances ranging from 670 to 860 nm and characterize SERS signatures of Gram-negative Escherichia coli and Serratia marcescens and Gram-positive Staphylococcus aureus and Staphylococcus epidermidis bacteria in water. Varying the concentration of bacteria and nanorods, we achieve large-area SERS enhancement that is independent of nanorod resonance and bacteria type; however, bacteria with higher surface charge density exhibit significantly higher SERS signal. Using cryo-electron microscopy and zeta potential measurements, we show that the higher signal results from attraction between positively charged nanorods and negatively charged bacteria. Our robust liquid-SERS measurements provide a foundation for bacterial identification and drug testing in biological fluids.

Interferon-gamma release assay for accurate detection of SARS-CoV-2 T cell response

We investigated feasibility and accuracy of an interferon-γ release assay (IGRA) for detection of T-cell responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Whole blood IGRA accurately distinguished between convalescent and uninfected healthy blood donors with a predominantly CD4⁺ T-cell response. SARS-CoV-2 IGRA may serve as a useful diagnostic tool in managing the coronavirus disease 2019 pandemic.

Simultaneous coccidioidomycosis and phaeohyphomycosis in a kidney transplant recipient: A case report and literature review

Advances in solid organ transplantation have improved the survival of end-stage organ disease at the expense of an increased risk for opportunistic infections. Unusual clinical presentations and the possibility of concurrent infections make diagnosing invasive fungal infection (IFI) more difficult. Here, we present a case of simultaneous vertebral infection caused by Coccidioides immitis-posadasii and subcutaneous phaeohyphomycosis due to Nigrograna mackinnonii in a kidney transplant recipient. The diagnosis of both infections required invasive procedures to obtain tissue and a high index of suspicion that more than one IFI could be present. A multidisciplinary team approach for the management of immunocompromised patients with suspected or diagnosed IFI is warranted.

A predictive tool for identification of SARS-CoV-2 PCR-negative emergency department patients using routine test results

Background

Testing for COVID-19 remains limited in the United States and across the world. Poor allocation of limited testing resources leads to misutilization of health system resources, which complementary rapid testing tools could ameliorate.

Objective

To predict SARS-CoV-2 PCR positivity based on complete blood count components and patient sex.

Study design

A retrospective case-control design for collection of data and a logistic regression prediction model was used. Participants were emergency department patients > 18 years old who had concurrent complete blood counts and SARS-CoV-2 PCR testing. 33 confirmed SARS-CoV-2 PCR positive and 357 negative patients at Stanford Health Care were used for model training. Validation cohorts consisted of emergency department patients > 18 years old who had concurrent complete blood counts and SARS-CoV-2 PCR testing in Northern California (41 PCR positive, 495 PCR negative), Seattle, Washington (40 PCR positive, 306 PCR negative), Chicago, Illinois (245 PCR positive, 1015 PCR negative), and South Korea (9 PCR positive, 236 PCR negative).

Results

A decision support tool that utilizes components of complete blood count and patient sex for prediction of SARS-CoV-2 PCR positivity demonstrated a C-statistic of 78 %, an optimized sensitivity of 93 %, and generalizability to other emergency department populations. By restricting PCR testing to predicted positive patients in a hypothetical scenario of 1000 patients requiring testing but testing resources limited to 60 % of patients, this tool would allow a 33 % increase in properly allocated resources.

Conclusions

A prediction tool based on complete blood count results can better allocate SARS-CoV-2 testing and other health care resources such as personal protective equipment during a pandemic surge.

Significance of bacterial and viral genotypes as a risk factor in driving cancer (Review)

Microbes have been known to drive human cancers for over half a century. However, despite the association of bacterial and viral infections with a high risk of cancer, most infections do not result in the development of cancer. Additionally, certain bacteria and viruses, considered to drive oncogenesis, are commonly prevalent in the global population. The current study performed a comprehensive meta-analysis of primary literature data to identify particular aspects of microbial genotypes as crucial factors that dictate the cancer risks associated with infection. The results indicated the importance of incorporating microbial genotype information with human genotypes into clinical assays for the more efficient diagnosis and prognosis of patients with cancer. The current review focuses on the importance of microbial genotypes and specific genes and genetic differences that are important to human oncogenesis.

Clinical Impact of Clostridium difficile PCR Cycle Threshold-Predicted Toxin Reporting in Pediatric Patients

BACKGROUND

Reliance on tests that detect only the presence of toxigenic Clostridium difficile can result in overdiagnosis and overtreatment of C difficile infection (CDI). The C difficile polymerase chain reaction (PCR) cycle threshold (CT) can sensitively predict the presence of free C difficile toxins; however, the clinical application for this testing strategy remains unexplored. We evaluated the impact of dual PCR and toxin result reporting, as predicted by the CT, on CDI management and outcomes in children.

METHODS

Before the intervention, results for C difficile testing at Lucile Packard Children's Hospital Stanford were reported as PCR positive (PCR+) or negative (PCR-) according to the GeneXpert C diff Epi tcdB PCR assay (Cepheid, Sunnyvale, California). Beginning October 5, 2016, the presence of free toxins, as predicted by the CT, was reported also. The CDI treatment rates 1 year before and 18 months after implementation of toxin reporting were compared. Demographic and treatment-related data were collected, and patient outcomes were followed up 8 weeks later.

RESULTS

CDI treatment decreased 22% after the intervention (96% [preintervention] vs 74% [postintervention]; P < .001). During the postintervention period, there were 152 PCR+C difficile results, and 94 (62%) of them were toxin positive (toxin+) according to the CT. Of the 58 PCR+/toxin-negative (toxin-) results, 38 (66%) did not result in CDI treatment. Seven (18%) of the untreated PCR+/toxin- patients underwent repeat testing within 8 weeks, and 5 (13%) of them were subsequently PCR+/toxin+ and treated. No CDI-related complications were identified.

CONCLUSIONS

Addition of the CT-predicted C difficile toxin result to PCR reporting reduces the proportion of PCR+ children treated for CDI.

Dual Reporting of Clostridioides difficile PCR and Predicted Toxin Result Based on PCR Cycle Threshold Reduces Treatment of Toxin-Negative Patients without Increases in Adverse Outcomes

Nucleic acid amplification tests are commonly used to diagnose Clostridioides difficile infection (CDI). Two-step testing with a toxin enzyme immunoassay is recommended to discriminate between infection and colonization but requires additional resources. Prior studies showed that PCR cycle threshold (CT ) can predict toxin positivity with high negative predictive value. Starting in October 2016, the predicted toxin result (CT-toxin) based on a validated cutoff was routinely reported at our facility. To evaluate the clinical efficacy of this reporting, all adult patients with positive GeneXpert PCR results from October 2016 through October 2017 underwent a chart review to measure the recurrence of or conversion to a CT-toxin+ result and 30-day all-cause mortality. There were 482 positive PCR tests in 430 unique patients, 282 CT-toxin+ and 200 CT-toxin- Patient characteristics were similar at testing, though CT-toxin+ patients had higher white blood cell (WBC) counts (12.5 × 103 versus 9.3 × 103 cells/μl; P = 0.001). All cases (n = 21) of fulminant CDI had a CT-toxin+ result. Index CT-toxin+ patients were significantly more likely to have a CT-toxin+ result within 90 days than CT-toxin- patients (17.4% [n = 49] versus 8.0% [n = 16], respectively; P = 0.003). Thirty-day all-cause mortality was higher in CT-toxin- patients (11.1% versus 6.8%; P = 0.1), though no deaths in CT-toxin- patients were directly attributable to CDI. Of the 200 CT-toxin- patients, 51.5% (n = 103) were treated for CDI. The rates of conversion to a CT-toxin+ result (8.8% versus 7.2%; P = 0.8) and all-cause mortality (8.8% versus 13.4%; P = 0.3) were similar between treated and untreated CT-toxin- patients, respectively. CT -based toxin prediction may identify patients at higher risk for CDI-related complications and reduce treatment among CT-toxin- patients.

645. Singulex Clarity Norovirus Assay (In Development) Provides Ultrasensitive Detection of Norovirus Genogroups I and II

Background

Commercially available enzyme immunoassays (EIAs) for detection of norovirus antigen have poor sensitivity and are limited to use in investigations of a gastroenteritis outbreak. Hence, there remains a need for a standalone high-sensitivity assay that enables rapid and accurate detection of norovirus antigen.

Methods

The Singulex Clarity norovirus assay is currently in development for use on the Singulex Clarity^® system (Singulex Inc., Alameda, CA, USA), a fully-automated platform powered by Single Molecule Counting technology (registered with the FDA and CE marked). The assay uses paramagnetic microparticles bound to capture antibody and a fluorescently labeled reporter antibody to detect virion capsid protein of norovirus genogroups I (GI) and II (GII) in the stool. For the development of Clarity Norovirus assay, diagnostic performance of 4 antibody pairs (as Capture and Detection reagent) were evaluated by testing 137 stool samples from patients with suspected norovirus infection. Samples were sourced from three providers: (1) 90 genotyped samples of which 75 were positive (19 different genotypes) and 15 were negative by the CDC assay, (2) 3 samples positive and 5 samples negative by the BioFire^® FilmArray^® Gastrointestinal Panel, and (3) 39 samples negative by a lab-developed test using Cepheid reagents (SmartCycler®).

Results

From all the antibody pairs tested, one of the pairs had best performance with the area under the receiver operating characteristic (AuROC) curve demonstrating a C-Statistic of 0.959 (95% CI 0.921–0.997), compared with AuROC C-statistic of 0.943 (95% CI 0.896–0.990), 0.871 (95% CI 0.807–0.936), and 0.914 (95% CI 0.863–0.964) for the three other pairs. The Clarity assay detected all 19 different genotypes tested (figures).

Conclusion

The ultrasensitive and rapid Clarity norovirus assay (in development) for detection of GI and GII demonstrated excellent performance with one of the antibody pairs tested and detected all 19 tested genotypes. The Clarity assay may offer a standalone solution for norovirus diagnostics.

Disclosures

All authors: No reported disclosures.

642. Higher Diagnostic Accuracy with Ultrasensitive Detection of Helicobacter pylori Stool Antigen Using Single-Molecule Counting Technology

Background

Current diagnostic methods for Helicobacter pylori infection include fecal antigen tests, ¹³C-urea breath test, and gastric biopsy. The breath test is limited by poor specificity and the fecal antigen tests by poor sensitivity. We have developed a prototype assay for detection of H. pylori antigen in human stool, powered by ultrasensitive Single Molecule Counting technology, and compared the analytical performance to a commercially available enzyme-linked immunoassay (EIA) antigen test.

Methods

The Singulex Clarity H. pylori antigen assay incubates diluted stool with capture and fluorescent-labeled detection antibodies. After incubation and wash steps, fluorescent molecules are eluted and single-molecule fluorescence measured by detected events (DE′). Analytical performance was compared with a commercial EIA (Premier Platinum HpSA^® Plus, Meridian Bioscience, Inc.) using serial dilutions of H. pylori control (~37,500–1.7 ng/mL) and high positive stool (signal to noise ratio >2). Clinical performance was evaluated using two cohorts, one had 10 EIA-negative and 10 EIA-positive samples and the other 13 high positives (> 0.500 at 450/630) and 5 low positives near the EIA cutoff (0.100–0.500 at 450/630). One sample was excluded due to discordant EIA results, and three to reader flags.

Results

The lower limit of detection of the Clarity H. pylori assay was 1.7 ng/mL and the EIA 1,250 ng/mL (IFU: LOD 4.67 ng/mL). A high positive stool sample was detectable by the Clarity H. pylori assay diluted 1:10,000,000 and by the EIA 1:10,000. The Clarity H. pylori assay showed a 729-fold increase in lower limit of detection and 1,000-fold increase in endogenous antigen lower limit of detection compared with the EIA. Clarity signal ranged from 46–665 DE’ for EIA-negative samples and 487,484–576,747 DE’ for EIA-positive samples.

Conclusion

The Singulex Clarity H. pylori antigen assay may have orders of magnitude higher analytical sensitivity than the commercial EIA and demonstrated 100% positive agreement and 100% negative agreement on detection of H. pylori antigen in human stool samples. The ultrasensitive Clarity H. pylori assay has the potential for high sensitivity and specificity to improve current diagnostic options for H. pylori infection; however, additional multicenter studies are required.

Disclosures

All authors: No reported disclosures.

Rapid and specific labeling of single live Mycobacterium tuberculosis with a dual-targeting fluorogenic probe

Tuberculosis (TB) remains a public health crisis and a leading cause of infection-related death globally. Although in high demand, imaging technologies that enable rapid, specific, and nongenetic labeling of live Mycobacterium tuberculosis (Mtb) remain underdeveloped. We report a dual-targeting strategy to develop a small molecular probe (CDG-DNB3) that can fluorescently label single bacilli within 1 hour. CDG-DNB3 fluoresces upon activation of the β-lactamase BlaC, a hydrolase naturally expressed in Mtb, and the fluorescent product is retained through covalent modification of the Mtb essential enzyme decaprenylphosphoryl-β-d-ribose 2'-epimerase (DprE1). This dual-targeting probe not only discriminates live from dead Bacillus Calmette-Guérin (BCG) but also shows specificity for Mtb over other bacterial species including 43 nontuberculosis mycobacteria (NTM). In addition, CDG-DNB3 can image BCG phagocytosis in real time, as well as Mtb in patients' sputum. Together with a low-cost, self-driven microfluidic chip, we have achieved rapid labeling and automated quantification of live BCG. This labeling approach should find many potential applications for research toward TB pathogenesis, treatment efficacy assessment, and diagnosis.

1H, 13C and 15N resonance assignments and structure prediction of translation initiation factor 1 from Clostridium difficile

Clostridium difficile is a gram-positive, toxin-producing, anaerobic bacterium whose virulence factors and mechanisms of pathogenesis require further investigation. C. difficile infections (CDI) result in the severe and potentially fatal gastrointestinal diseases pseudomembranous colitis and toxic megacolon following extensive broad spectrum antibiotic treatment. The increasing C. difficile fatalities are a result of the bacteria's growing antibiotic resistance and consequential CDI recurrence, which led to the unmet need for new CDI treatment. Bacterial protein synthesis is an essential metabolic process and an effective target for antibacterial agents. Translation initiation factor 1 from C. difficile (Cd-IF1) is the smallest of the three initiation factors that acts to establish the 30S initiation complex to initiate translation during protein biosynthesis. Here we report the complete NMR ¹H, ¹³C and ¹⁵N chemical shift assignments of Cd-IF1 as the basis for NMR structure determination and interaction studies. Secondary structure analyses have identified five β-strands and one short α-helix arranged in the sequential order β1-β2-β3-α1-β4-β5, which is supported by ¹⁵N-{¹H} heteroNOEs. The assigned chemical shifts were used to conduct structure prediction by CS-Rosetta. The predicted structure suggests that Cd-IF1 adopts the typical β-barrel structure and is composed of an oligomer-binding motif.

Reproducibility of positive results for rare pathogens on the FilmArray GI Panel

Though the FilmArray GI Panel has a reported aggregate specificity and reproducibility of >97% and > 99%, respectively, the reproducibility is less understood in clinical practice. We measured the reproducibility of positive results for low-prevalence pathogens. Samples with positive results for selected targets were repeated using a different FilmArray module. Overall, 331 of 373 (89%) results were reproducible. Giardia lamblia (57/57, 100%), Cryptosporidium spp. (61/63, 97%), Cyclospora cayetanensis (34/35, 97%), Plesiomonas shigelloides (17/18, 94%), and Rotavirus A (76/77, 99%) were highly reproducible, while Adenovirus F40/41 (38/54, 70%), Vibrio spp. (8/10, 80%), V. cholerae (3/8, 37.5%), and Yersinia enterocolitica (36/50, 72%) were poorly reproducible. Review of 38 patients with nonreproducible results showed that 19 (50%) had evidence of gastroenteritis and only 6 (16%) had possible infection with the organism that showed a nonreproducible result. Higher false-positive rates with certain targets on FAGP emphasize the need for diagnostic stewardship.

Eremothecium coryli bloodstream infection in a patient with acute myeloid leukemia: first case report of human infection

Eremothecium coryli is a dimorphic fungus of the Saccharomycetes class. While species within this class are known to cause human infection, Eremothecium species have previously only been known as phytopathogens and never been isolated from a human sample. Here, we report the first known case of human E. coryli infection.

Rapid antimicrobial susceptibility testing by VITEK®2 directly from blood cultures in patients with Gram-negative rod bacteremia

OBJECTIVE

Optimizing therapy for bacteremia is currently limited by the 1-2-day turnaround time required for antimicrobial susceptibility testing (AST). Here, we assess a rapid AST method with VITEK®2 (bioMérieux, France) directly from positive blood cultures.

METHODS

Patient-derived positive blood cultures with Gram-negative rods identified as Enterobacteriaceae and Pseudomonas aeruginosa were prospectively tested, and other blood culture bottles were spiked with carbapenem-resistant Enterobacteriaceae (CRE). Positive cultures were subjected to red blood cell lysis and centrifugation, and setup on VITEK®2.

RESULTS

A total of 109 patient blood cultures and 52 spiked blood cultures were tested. Overall, essential agreement was 97.7% [95% confidence interval (CI) 96.4-99.0], and categorical agreement was 96.8% (95% CI 95.0-98.6). Mean turnaround time from setup to susceptibility results for Enterobacteriaceae in the clinical cultures was 9.0 (±1.3) h.

CONCLUSIONS

Direct susceptibility testing of blood cultures by VITEK®2 for Enterobacteriaceae is an accurate, practical, and inexpensive diagnostic strategy for rapid automated AST.

2067. Novel Methodology for Same-Day Antimicrobial Susceptibility Testing on VITEK®2 for Gram-Negative Rod Bacteremia

Background

Bloodstream infections with Gram-negative rods are potentially fatal and require tailored antimicrobial treatment. Optimizing therapy is currently limited by the 1–2 days turnaround time required for antimicrobial susceptibility testing. Novel same-day technologies have been developed but are expensive. Here, we describe and investigate the accuracy of a repurposed existing technology (VITEK^®2, bioMérieux) for same-day susceptibility testing directly from positive blood cultures.

Methods

Starting in August 2017, patients with blood cultures positive for Gram-negative rods were prospectively included. In addition, aerobic and anaerobic blood culture bottles were spiked with a standardized inoculum of enteric Gram-negative rods from a repository of frozen samples. Positive blood cultures were processed using a newly developed protocol based on red blood cell lysis and differential centrifugation of bacteria, followed by VITEK^®2 card set-up. VITEK^®2 results from the direct method were compared with a reference method (VITEK^®2 results using a 24-hour colony).

Results

In the prospective study, a total of 109 nonduplicate samples were collected, with E. coli (n = 54) and Klebsiella pneumoniae (n = 51) the main pathogens detected. In addition, a total of 52 blood culture bottles were spiked with resistant Gram-negative rods. Overall weighted essential agreement was 98.8%, and categorical agreement was 97.9% between the direct and reference methods. Accurate results were produced for the main antibiotics used to treat enteric Gram-negative bacteremia, including ceftriaxone, piperacillin–tazobactam and meropenem. Mean turnaround time to susceptibility results for Enterobacteriaceae in the prospective study was 9.0 (±1.3) hours.

Conclusion

Preliminary data from direct antimicrobial susceptibility testing by VITEK^®2 for enteric Gram-negative rod bacteremia suggest this technique is accurate, practical, easily integrated in the laboratory workflow, and substantially cheaper than its competitor technology. The next phase of this study will assess the impact of faster antimicrobial susceptibility turnaround time on patient outcomes and antimicrobial stewardship targets.

Disclosures

All authors: No reported disclosures.

1092. Tuning Down Clostridioides difficile PCR Sensitivity Reduces Treatment for C. difficile Infection in Toxin-Negative Patients With No Increase in Adverse Outcomes

Background

Studies have shown that toxin detection identifies those who require treatment for C. difficile infection (CDI) and free toxin can be predicted with high negative predictive value from PCR cycle threshold (CT). CT-toxin was introduced at our institution in two phases: from October 2016 to October 2017, CT-toxin was reported with the PCR result (split reporting) and CDI therapy was discouraged if CT-toxin was negative (PCR+/CTtox−). Interim analysis showed that CDI treatment had no effect on outcomes in these CTtox− patients, so starting November 2017, only CT-toxin was reported. Outcomes in PCR+/CTtox− patients treated during split reporting and untreated during the toxin-only period are detailed here.

Methods

Patients tested from October 2016 to February. 2018 with a positive Xpert tcdB PCR (Cepheid, Sunnyvale, CA) and CTtox− result were included. Clinical data were collected by retrospective chart review in the split reporting period and prospective review in the toxin-only period and analyzed using SPSS at α = 0.01.

Results

Of 186 unique PCR+/CTtox- patients during split reporting, 99 (53%) were treated, compared with 6 (12%, n = 51) in the toxin-only period (P < 0.001). In comparing treated patients during split reporting to untreated patients during toxin-only reporting (n = 45), there were no significant differences in age, sex, prior antibiotic use, CDI in the previous 6 months, Charlson Comorbidity Index, patient location, immune status, or data at testing, including WBC count, creatinine, albumin, and stools/day. There were no cases of fulminant CDI in either group and no difference in outcomes (table).

Conclusion

Reporting of CT-toxin alone significantly reduced treatment for CDI compared with split reporting in CTtox− patients with no increase in adverse outcomes in short-term follow-up. Further study is needed to confirm these findings in a larger cohort.

Disclosures

All authors: No reported disclosures.

Precision identification of diverse bloodstream pathogens in the gut microbiome

A comprehensive evaluation of every patient with a bloodstream infection includes an attempt to identify the infectious source. Pathogens can originate from various places, such as the gut microbiome, skin, and external environment. Identifying the definitive origin of an infection would enable precise interventions focused on management of the source^1,2. Unfortunately, hospital infection control practices are often informed by assumptions about the source of various specific pathogens; if these assumptions are incorrect they lead to interventions that do not decrease pathogen exposure³. Here, we develop and apply a streamlined bioinformatic tool, named StrainSifter, to match bloodstream pathogens precisely to a candidate source. We then leverage this approach to interrogate the gut microbiome as a potential reservoir of bloodstream pathogens in a cohort of hematopoietic cell transplantation recipients. We find that patients with Escherichia coli and Klebsiella pneumoniae bloodstream infections have concomitant gut colonization with these organisms, suggesting that the gut may be a source of these infections. We also find cases where classically non-enteric pathogens, such as Pseudomonas aeruginosa and Staphylococcus epidermidis, are found in the gut microbiome, thereby challenging existing informal dogma of these infections originating from environmental or skin sources. Thus, we present an approach to distinguish the source of various bloodstream infections, which may facilitate more accurate tracking and prevention of hospital-acquired infections.

Diversity of resistance mechanisms in carbapenem-resistant Enterobacteriaceae at a health care system in Northern California, from 2013 to 2016

The mechanism of resistance in carbapenem-resistant Enterobacteriaceae (CRE) has therapeutic implications. We comprehensively characterized emerging mechanisms of resistance in CRE between 2013 and 2016 at a health system in Northern California. A total of 38.7% (24/62) of CRE isolates were carbapenemase gene-positive, comprising 25.0% (6/24) bla_{OXA-48 like}, 20.8% (5/24) bla_KPC, 20.8% (5/24) bla_NDM, 20.8% (5/24) bla_SME, 8.3% (2/24) bla_IMP, and 4.2% (1/24) bla_VIM. Between carbapenemases and porin loss, the resistance mechanism was identified in 95.2% (59/62) of CRE isolates. Isolates expressing bla_KPC were 100% susceptible to ceftazidime-avibactam, meropenem-vaborbactam, and imipenem-relebactam; bla_{OXA-48 like}-positive isolates were 100% susceptible to ceftazidime-avibactam; and metallo β-lactamase-positive isolates were nearly all nonsusceptible to above antibiotics. Carbapenemase gene-negative CRE were 100% (38/38), 92.1% (35/38), 89.5% (34/38), and 31.6% (12/38) susceptible to ceftazidime-avibactam, meropenem-vaborbactam, imipenem-relebactam, and ceftolozane-tazobactam, respectively. None of the CRE strains were identical by whole genome sequencing. At this health system, CRE were mediated by diverse mechanisms with predictable susceptibility to newer β-lactamase inhibitors.

Liquid biopsy for infectious diseases: sequencing of cell-free plasma to detect pathogen DNA in patients with invasive fungal disease

Diagnosis of life-threatening deep-seated infections currently requires invasive sampling of the infected tissue to provide a microbiologic diagnosis. These procedures can lead to high morbidity in patients and add to healthcare costs. Here we describe a novel next-generation sequencing assay that was used to detect pathogen-derived cell-free DNA in peripheral blood of patients with biopsy-proven invasive fungal infections. The noninvasive nature of this approach could provide rapid, actionable treatment information for invasive fungal infections when a biopsy is not possible.

Development of colorimetric sensor array for diagnosis of tuberculosis through detection of urinary volatile organic compounds

BACKGROUND

Top priorities for tuberculosis control and elimination include a simple, low-cost screening test using sputum and a non-sputum-based test in patients that do not produce sputum. The aim of this study was to evaluate the performance of a colorimetric sensor array (CSA) test, for analysis of volatile organic compounds in urine, in the diagnosis of pulmonary TB.

MATERIAL AND METHODS

Urine samples were collected from individuals suspected of having pulmonary TB in Western Kenya. Reference methods included MGIT culture and/or Xpert MTB/RIF nucleic acid amplification test on sputa. Fresh urine samples were tested with the CSA, with acid and base and without an additive. The CSA were digitally imaged, and the resulting colorimetric response patterns were used for chemometric analysis. Sensitivity, specificity, and negative (NPV) and positive predictive (PPV) values were determined for HIV-positive and HIV-negative patients.

RESULTS

In HIV-negative patients, the highest accuracy was obtained in urine samples pre-treated with a base, yielding a sensitivity, specificity, PPV, and NPV of 78.3% (65/83), 69.2% (54/78), 73.0% (n/89) and 75.0% (n/72). The highest sensitivity of 79.5% was achieved using sensor data from all three test conditions at a specificity of 65.4%. In HIV-positive subjects, the sensor performance was substantially lower with sensitivity, specificity, PPV, and NPV ranging from 48.3% to 62.3%, 54.1% to 74.0%, 55.9% to 64.2%, and 60.6% to 64.9%, respectively.

CONCLUSION

The CSA fingerprint of urine headspace volatiles showed moderate accuracy in diagnosing TB in HIV-negative patients, but the sensor performance dropped substantially in HIV-coinfected patients. Further development of TB-responsive CSA indicators may improve the accuracy of CSA urine assay.

Fatal Emmonsia sp. Infection and Fungemia after Orthotopic Liver Transplantation

We report a fatal case of disseminated Emmonsia sp. infection in a 55-year-old man who received an orthotopic liver transplant. The patient had pneumonia and fungemia, and multisystem organ failure developed. As human habitats and the number of immunocompromised patients increase, physicians must be aware of this emerging fungal infection.

Intramolecular substitution uncages fluorogenic probes for detection of metallo-carbapenemase-expressing bacteria

This work reports a novel caging strategy for designing fluorogenic probes to detect the activity of β-lactamases. The caging strategy uses a thiophenyl linker connected to a fluorophore caged by a good leaving group-dinitrophenyl. The uncaging proceeds in two steps through the sulfa-releasing and subsequent intramolecular substitution. The length of the linker has been examined and optimized to maximize the rate of intramolecular reaction and thus the rate of fluorescence activation. Finally based on this strategy, we prepared a green fluorogenic probe CAT-7 and validated its selectivity for detecting metallo-carbapenemases (VIM-27, IMP-1, NDM-1) in carbapenem-resistant Enterobacteriaceae (CRE) lysates.

PCR Cycle-Threshold-Derived Toxin Identifies Patients at Low-Risk for Complications of C. difficile Infection Who Do Not Require Treatment

Background

Literature suggests that toxin detection differentiates those who require treatment for C. difficile infection (CDI) from those who do not. In-house studies have shown that free toxin can be predicted with high negative predictive value at a predefined cycle threshold (CT) using Xpert tcdB PCR (Cepheid, Sunnyvale, CA). In October 2016, CT-toxin was added to the PCR result and a comment recommends against CDI therapy if CT-toxin is negative (CTtox-). Here we evaluate the effect of this reporting on treatment rates and outcomes of CTtox- patients.

Methods

Patients tested from October 2016 to Apr. 2017 with a positive Xpert PCR and CTtox- result were included. Clinical data were collected by retrospective chart review and analyzed with the Chi squared and Student t-tests using SPSS. Due to multiple comparisons, α=0.01.

Results

Of 1516 Xpert PCR tests, 248 (16.4%) were positive and 98 (39.5%) were CTtox-. Of these, 54 (55.7%) were treated. Patient characteristics and data at testing are shown below. There were no cases of CDI-related septic shock or toxic megacolon on review. Time to diarrhea resolution was significantly shorter in untreated patients and there was no difference in crude mortality or later onset of CTtox+ CDI.

Conclusion

This study demonstrates the impact of stand-alone PCR assay with toxin prediction on reducing CDI therapy rates and provides further evidence that PCR+/toxin- patients are at low risk for CDI-related complications and do not require treatment, though more data is needed in transplant populations.

Disclosures

N. Banaei, Cepheid: Collaborator, Research Contractor and Scientific Advisor, honorarium for advisory role and Research support

Strain-level Determination of the Contribution of Gut Microbiota to the Development of Bacteremia in Patients Undergoing Stem Cell Transplantation

Background

Infection is a major preventable cause of transplant-related morbidity and mortality in patients undergoing hematopoietic stem cell transplantation (HCT). Bacteremia is the most common infectious complication in HCT, often occurring during periods of mucositis when the risk for microbial translocation from the intestine is increased. Prior research in HCT patients using 16S rRNA sequencing demonstrated that gut microbiota dominance by either Enterococcus spp. or Proteobacteria was associated with the development of bacteremia with Enterococcus spp. and Gram-negative organisms, respectively. No studies to date, however, have compared bacteremia isolates and gut microbiota samples at a strain-specific level using next-generation shotgun metagenomic sequencing (NGS).

Methods

In order to assess the degree of genetic similarity between bacteremia isolates and the gut microbiota, we identified patients who had undergone HCT at Stanford and developed a bacteremia between October 2015 and September 2016 for whom we had both saved blood culture isolates and stool samples within 30 days preceding bacteremia. We identified 15 patients from whom we had 17 bacteremia isolates, and performed NGS (Illumina HiSeq 4000) on stool and isolate DNA. We generated draft assemblies of isolate genomes using the SPAdes assembler, and aligned stool metagenomic reads to the draft isolate genomes using Bowtie2, filtering reads for perfect end-to-end alignment.

Results

Enteric gram-negative bacteremia isolates were identical to those in the gut microbiota, as has been demonstrated in prior studies using older strain-typing Methods. Surprisingly, we also identified gram-positive organisms that were identical in both the blood and stool prior to bacteremia, which challenges existing dogma regarding sources of gram-positive bacteremia-causing organisms.

Conclusion

Using a highly sensitive and accurate NGS-based strain typing method, we provide evidence of translocation of organisms from the gut microbiota and subsequent bacteremia. The gut was confirmed as a source for both classic enteric gram-negative and classically non-enteric Gram-positive bacteremia in HCT patients. These findings may have implications for the origins of bacteremia in HCT patients previously classified as CLABSIs.

Disclosures

A. Bhatt, Janssen Human Microbiome Institute / Johnson and Johnson: Consultant, Consulting fee

Malaria and Chikungunya Detected Using Molecular Diagnostics Among Febrile Kenyan Children

BACKGROUND

In sub-Saharan Africa, malaria is frequently overdiagnosed as the cause of an undifferentiated febrile illness, whereas arboviral illnesses are presumed to be underdiagnosed.

METHODS

Sera from 385 febrile Kenyan children, who presented to 1 of 4 clinical sites, were tested using microscopy and real-time molecular assays for dengue virus (DENV), chikungunya virus (CHIKV), malaria, and Leptospira.

RESULTS

Malaria was the primary clinical diagnosis for 254 patients, and an arboviral infection (DENV or CHIKV) was the primary diagnosis for 93 patients. In total, 158 patients (41.0%) had malaria and 32 patients (8.3%) had CHIKV infections. Compared with real-time polymerase chain reaction, microscopy demonstrated a percent positive agreement of 49.7%. The percentage of malaria cases detected by microscopy varied significantly between clinical sites. Arboviral infections were the clinical diagnosis for patients on the Indian Ocean coast (91 of 238, 38.2%) significantly more often than patients in the Lake Victoria region (2 of 145, 1.4%; P < .001). However, detection of CHIKV infections was significantly higher in the Lake Victoria region (19 of 145 [13.1%] vs 13 of 239 [5.4%]; P = .012).

CONCLUSIONS

The clinical diagnosis of patients with an acute febrile illness, even when aided by microscopy, remains inaccurate in malaria-endemic areas, contributing to inappropriate management decisions.

New and developing diagnostic technologies for urinary tract infections

Timely and accurate identification and determination of the antimicrobial susceptibility of uropathogens is central to the management of UTIs. Urine dipsticks are fast and amenable to point-of-care testing, but do not have adequate diagnostic accuracy or provide microbiological diagnosis. Urine culture with antimicrobial susceptibility testing takes 2-3 days and requires a clinical laboratory. The common use of empirical antibiotics has contributed to the rise of multidrug-resistant organisms, reducing treatment options and increasing costs. In addition to improved antimicrobial stewardship and the development of new antimicrobials, novel diagnostics are needed for timely microbial identification and determination of antimicrobial susceptibilities. New diagnostic platforms, including nucleic acid tests and mass spectrometry, have been approved for clinical use and have improved the speed and accuracy of pathogen identification from primary cultures. Optimization for direct urine testing would reduce the time to diagnosis, yet these technologies do not provide comprehensive information on antimicrobial susceptibility. Emerging technologies including biosensors, microfluidics, and other integrated platforms could improve UTI diagnosis via direct pathogen detection from urine samples, rapid antimicrobial susceptibility testing, and point-of-care testing. Successful development and implementation of these technologies has the potential to usher in an era of precision medicine to improve patient care and public health.

Delayed Diagnosis of Tuberculous Meningitis Misdiagnosed as Herpes Simplex Virus-1 Encephalitis With the FilmArray Syndromic Polymerase Chain Reaction Panel

The FilmArray meningitis/encephalitis (ME) panel is a novel syndromic, nucleic acid amplification test for diagnosis of acute meningitis and encephalitis. Emerging data on its performance are concerning for false-positive results. We present a case of tuberculous meningitis misdiagnosed as herpes simplex virus-1 encephalitis with the FilmArray ME panel. Strategies to mitigate erroneous results are discussed.

Are Cystic Fibrosis Aspergillus fumigatus Isolates Different? Intermicrobial Interactions with Pseudomonas

Pseudomonas aeruginosa and Aspergillus fumigatus are the leading bacterial and fungal pathogens in cystic fibrosis (CF). We have shown that Af biofilms are susceptible to Pseudomonas, particularly CF phenotypes. Those studies were performed with a reference virulent non-CF Aspergillus. Pseudomonas resident in CF airways undergo profound genetic and phenotypic adaptations to the abnormal environment. Studies have also indicated Aspergillus from CF patients have unexpected profiles of antifungal susceptibility. This would suggest that Aspergillus isolates from CF patients may be different or altered from other clinical isolates. It is important to know whether Aspergillus may also be altered, as a result of that CF environment, in susceptibility to Pseudomonas. CF Aspergillus proved not different in that susceptibility.

Modification of the Epoxy Resin Mechanical and Thermal Properties with Silicon Acrylate and Montmorillonite Nanoparticles

In this study we have investigated the effect of montmorillonite with alkyl quaternary ammonium salt that had been doped into the silicon acrylate (AC-Si)/ Epoxy Cresol Novolac (ECN)/ montmorillonite nano composites on structural, mechanical and thermal properties of composite samples. Moreover the effect of increase in weight percentages of fillers at 0.01, 0.02, 0.03 and 0.04 wt% on the amount of Impact and flexural strength had been investigated. Also impact and flexural strength were performed on two different systems namely (a) ECN filled nanoclay and (b) AC-Si ECN filled with nano montmorillonite as a function of clay respectively. By increase in the weight percentage of filler in the context of matrix up to the 0.03 wt%, the amount of flexural and impact strength were increased but by adding filler more that 0.03 wt%, the amount of flexural and impact strength will decrease. The resulting nanocomposites have optimal mechanical properties at 0.03 wt% montmorillonite content. Addition of The AC-Si will increase the interlamellar distance due to better dispersion of the clay within the matrix. Cross section of fracture surfaces that had been shown by SEM micrographs, specifies that, increase in viscosity had caused due to aggregation that is the main cause of fluctuation in samples properties. In addition the produced samples were characterized by X-ray diffraction (XRD) differential scanning calorimetry, Thermal gravimetric analysis, scanning electron microscopy and mechanical testing (impact and flexural).

Rapid Diagnosis of Tuberculosis from Analysis of Urine Volatile Organic Compounds

The World Health Organization has called for simple, sensitive, and non-sputum diagnostics for tuberculosis. We report development of a urine tuberculosis test using a colorimetric sensor array (CSA). The sensor comprised of 73 different indicators captures high-dimensional, spatiotemporal signatures of volatile chemicals emitted by human urine samples. The sensor responses to 63 urine samples collected from 22 tuberculosis cases and 41 symptomatic controls were measured under five different urine test conditions. Basified testing condition yielded the best accuracy with 85.5% sensitivity and 79.5% specificity. The CSA urine assay offers desired features needed for tuberculosis diagnosis in endemic settings.