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.

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.