bluuebunny/crossref_metadata_2025 huggingface dataset:
1202. Subinhibitory Concentrations of Omadacycline Inhibit Staphylococcus aureus Hemolytic Activity in Vitro
Authors: Serio Alisa W , Tanaka S Ken , Wright Kelly , Garrity-Ryan Lynne
Published: January 2021

Background

In animal models of Staphylococcus aureus infection, α-hemolysin has been shown to be a key virulence factor. Treatment of S. aureus with subinhibitory levels of protein synthesis inhibitors can decrease α-hemolysin expression. Omadacycline, a novel aminomethylcycline antibiotic in the tetracycline class of bacterial protein biosynthesis inhibitors, is approved in the United States for treatment of community-acquired bacterial pneumonia (CABP) and acute bacterial skin and skin structure infections (ABSSSI) in adults. This study was performed to determine the durability of inhibition and effect of subinhibitory concentrations of omadacycline on S. aureus hemolytic activity.

Methods

All experiments used the methicillin-sensitive S. aureus strain Wood 46 (ATCC 10832), a laboratory strain known to secrete high levels of α-hemolysin. Minimum inhibitory concentrations (MICs) of omadacycline and comparator antibiotics (tetracycline, cephalothin, clindamycin, vancomycin, linezolid) were determined. Growth of S. aureus with all antibiotics was determined and the percentage of hemolysis assayed. “Washout” experiments were performed with omadacycline only.

Results

S. aureus cultures treated with 1/2 or 1/4 the MIC of omadacycline for 4 hours showed hemolysis units/108 CFU of 47% and 59% of vehicle-treated cultures, respectively (Fig. 1A, 1B). In washout experiments, treatment with as little as 1/4 the MIC of omadacycline for 1 hour decreased the hemolysis units/108 CFU by 60% for 4 hours following removal of the drug (Table 1).

Figure 1

Table 1

Conclusion

Omadacycline inhibited S. aureus hemolytic activity in vitro at subinhibitory concentrations and inhibition was maintained for ≥ 4 hours after removal of extracellular drug (Fig. 2). The suppression of virulence factors throughout the approved omadacycline dosing interval, in addition to the in vitro potency of omadacycline, may contribute to the efficacy of omadacycline for ABSSSI and CABP due to virulent S. aureus. This finding may apply to other organisms and other virulence factors that require new protein synthesis to establish disease.

Figure 2

Disclosures

Alisa W. Serio, PhD, Paratek Pharmaceuticals, Inc. (Employee, Shareholder) S. Ken Tanaka, PhD, Paratek Pharmaceuticals, Inc. (Employee, Shareholder) Kelly Wright, PharmD, Paratek Pharmaceuticals, Inc. (Employee, Shareholder) Lynne Garrity-Ryan, PhD, Paratek Pharmaceuticals, Inc. (Employee, Shareholder)
1203. Systemic, Mucosal Immune Activation And Psycho-sexual Health in HIV-Infected And Uninfected Women: Evaluation of Biomarkers And Environmental Stimuli
Authors: Nijhawan Parni , Nijhawan Parni , Carraro Anna , Marocco raffaella , Vita Serena , Kertusha Blerta , Mascia Claudia , Lichtner Miriam , Mastroianni Claudio , Zingaropoli Maria Antonella , Masci Georgio , Ianiri Palmieri , Vito Mercurio , Fondaco Laura , Del Borgo Cosmo , Mirella D’Achille
Published: January 2021

Background

HIV infection in women in disproportionate ratios as compared to men has been a grave concern over the years. It is in proportion to reproductive and hormonal differences making women more vulnerable. It elicits an Immune response which can be monitored by analysing various factors such as mucosal immunity, sexual behaviour, biomarkers in the plasma, serum and vaginal lavage and vaginal infections.

Aim

Evaluating and comparing the systemic and mucosal immuno-inflammatory status, the female sexual function (FSF) and generalized anxiety in HIV+ women on successful HAART with healthy women (HW).

Methods

We enrolled 53 subjects (23 HIV+ women on successful HAART and 30 Healthy women (HW)) with no statistical differences in age. The figure (named: methodology) below explains the methods applied:

Cytometry and Kit ELISA were used to estimate lymphocytes and all cytokines. Women were also tested for co-morbidities such as diabetes, blood pressure, HCV, cervical cancer etc. Statistical analysis was performed using PRISM 8.0.

Methodology

Results

Higher CD4 and CD8 cell count was observed in HW compared to HIV+ women (p=0.02,p=0.004).Plasma levels of sCD 163, CXCL-10, IL-1, IL-6 and IL-8 were significantly higher in HIV women as compared to HW(p< 0.001), while IL-6 and IL8 were lower in the VL of HIV women. An ASCUS in HW was found for PAP Test. CXCL-10 was correlated to estradiol levels (r=0.8, p=0.02). 57% reported FSD and 43% had a FSFI score≤10. A significant difference between the two groups in the FSFI score (p=0.007) was found, particularly in sexual desire, arousal and pain. A positive correlation between level of testosterone and FSFI score was found only in HIV+ women (p=0.02; r= 0.74). 17% of women presented an anxiety disorder. Z-index was associated with orgasm domains (p=0.01; r=-0.4) and CD4+ T cells (p=0.02; r=-0.45).

Conclusion

Higher plasma levels of the cytokines despite successful antiretroviral therapy were observed. At the mucosal level evaluating the balance within pro anti-inflammatory cytokines and micro-biome will be interesting to study. FSD is detected in more than half of HIV infected women and seems to be related to testosterone levels. The comparison with uninfected women underlying a persistent gap in quality of life of young HIV women should be bridged.

Disclosures

All Authors: No reported disclosures
1204. The Effect of Coinfection with Babesiosis and Lyme Disease on Novel Biomarkers
Authors: Lum Michael D , Reardon Kelsey , Spector Rachel , Garry Evan , Papamanoli Aikaterini , Marcos Luis
Published: January 2021

Background

Current literature presents conflicting results regarding the clinical manifestations of coinfection with Babesia microti (Babesiosis) and Borrelia burgdorferi (Lyme disease). The aim of this study is to investigate the effect that coinfection with Babesiosis and Lyme Disease has on standard and novel biomarkers markers such as C-reactive protein (CRP), erythrocyte sedimentation rate (ESR) and procalcitonin (Pc), which may assist in elucidating how these pathogens interact within human hosts.

Methods

Babesia cases were collected from Stony Brook University Hospital from 2012 to 2019. Cases of Babesia were included if parasites were detected by peripheral blood smear and confirmed by PCR. Lyme disease diagnosis criteria involved 2-tier testing per CDC guidelines. Cases were divided into three cohorts based on if they had CRP, ESR or Pc tested. Cohorts were divided into two groups: Babesiosis alone vs coinfection with Lyme Disease. Median values were analyzed for the following biomarkers across both groups: parasitemia, hemoglobin (Hgb), white blood cells (WBC), platelets, indirect bilirubin (IB), lactate dehydrogenase, ESR, CRP and Pc. Fisher Exact and Wilcoxon Rank sum tests were used and P values < 0.05 were considered statistically significant.

Results

ESR values trended higher in monoinfection compared to coinfection (50 vs 36 mm/hr, p=0.63). Within this cohort, the coinfection group had significantly lower platelet values compared to monoinfection (52 vs. 75.5 K/uL, p=0.04, Table 1). Within the CRP and Pc cohorts, monoinfection had higher trends of parasitemia compared to coinfection (CRP group: 1.6 vs 0.7%, p=0.14, Pc group: 1.4 vs 0.7% p=1.0, Table 2&3). Pc levels were similar in both groups (1.1 vs 1.2 ng/mL, p=1.0, Table 3).

Table 1: Demographics and Biomarkers for Patients with Babesiosis Monoinfection vs. Coinfection with Babesiosis and Lyme Disease that had ESR Measured.

Table 2: Demographics and Biomarkers for Patients with Babesiosis Monoinfection vs. Coinfection with Babesiosis and Lyme Disease that had CRP Measured.

Table 3: Demographics and Biomarkers for Patients with Babesiosis Alone vs Coinfection with Babesiosis and Lyme Disease that had Procalcitonin Measured.

Conclusion

Coinfection had significantly lower platelets within the ESR cohort but not in other cohorts. While not statistically significant, monoinfection showed greater trends of ESR and parasitemia, which is consistent with previous studies that suggest that

B. burgdorferi may mitigate the effects of B. microti infection. CRP and Pc levels were similar across both groups suggesting that the utility of using novel biomarkers to elucidate the interaction between B. burgdorferi and B. microti during simultaneous infection requires further study.

Disclosures

All Authors: No reported disclosures
94. Appropriate Urine Legionella Antigen Testing: A Step Towards Diagnostic Stewardship
Authors: Ahmad Faran , Ahmed Moeed , Velagapudi Manasa , Bittner Marvin J
Published: January 2021

Background

Pneumonia is a leading cause of sepsis and hospitalization. Infectious Diseases Society of America and American Thoracic Society (IDSA/ATS) published 2019 practice guidelines for community-acquired pneumonia (CAP), recommending urinary antigen testing (UAT) for Legionella pneumophila (LP) only in patients with severe pneumonia or having epidemiological risk factors. In the last 20 years, there has been no Legionella outbreak in Nebraska. Currently, the urine antigen test is considered based on the discretion of the ordering provider. However, this usually results in over-utilization of the test and associated financial burden.

Methods

Retrospective chart review of patients admitted to Bergan Mercy Medical Center, Creighton University, Omaha with the admission diagnosis of community-acquired pneumonia in the year 2019, by using electronic medical records. The charts were reviewed for baseline characteristics, admission diagnoses, and clinical outcomes. The project was submitted to and reviewed by the institutional review board.

Results

From January to December 2019, 4738 patients were admitted to the general medical floors with the diagnosis of community-acquired pneumonia. Among those patients, 826 patients (17.43%) had urine Legionella antigen tests done, only 11 (0.23%) were tested positive. Moreover, 140 patients (2.95%) had urine Legionella antigen tests in the absence of a documented diagnosis of community-acquired pneumonia. Patients admitted to intensive care units were not included in the study as guidelines do not restrict from ordering urine Legionella tests in patients with severe sepsis secondary to community-acquired pneumonia.

Conclusion

A diagnostic stewardship approach should be considered for urine Legionella antigen testing. Moreover, such a retrospective review provides an opportunity for quality improvement initiatives at the academic medical facilities with lower Legionella outbreaks.

Disclosures

All Authors: No reported disclosures
1208. Development of a Novel Synthetic Glycan to Prevent Bacterial Infections and Ameliorate Respiratory Viral Infections
Authors: Meisner Jeffrey , Lee Jackson , Lawrence Jonathan , Roed Megan , Vlieg Johan van Hylckama
Published: January 2021

Background

The prevention and treatment of bacterial infections is a human health challenge. A disadvantage of antibiotics is that they often kill beneficial commensal, bacteria in addition to, pathogenic bacteria. Indiscriminate killing disrupts the homeostasis between commensal bacteria and the host gut epithelium allowing colonization of the gut by pathogenic bacteria and increases susceptibility to infections. This research was done to develop a non-antibiotic modality to prevent bacterial infections by growing, rather than killing, commensal bacteria in the gut. Gut commensal bacteria grown on carbohydrates produce short-chain fatty acids (SCFAs) that support gut homeostasis maintenance and promote resistance to bacterial colonization. SCFAs have direct and indirect effects on the gut and lung mucosal immune system. They have also been linked to respiratory viral infection reduction and shown to influence macrophage function to mitigate pro-inflammatory neutrophil-mediated tissue damage.

Methods

A library of over 1,500 synthetic proprietary glycans, termed Microbiome Metabolic Therapies (MMT™), was synthesized using different chemical and enzymatic approaches. An ex vivo platform using fecal bacterial communities from human subjects was devised to screen MMTs for their abilities to deplete pathogenic bacteria, and modulate multiple aspects of bacterial metabolism.

Results

KB109 was identified based on its ability to reduce the relative abundance of a diversity of pathogens including clinically relevant Gram-negative and Gram-positive bacteria in human fecal communities. KB109 also increased the relative abundance of prevalent commensal bacteria. Monoculture experiments demonstrated that KB109 promotes the growth of commensal bacteria, but not pathogens. Ex vivo screening revealed that KB109 consistently increased SFCA production across multiple fecal communities.

Conclusion

KB109 represents an appealing activity profile and offers an opportunity to prevent enteric and systemic bacterial infections by promoting gut homeostasis and colonization resistance, and ameliorating respiratory viral infections by stimulating immune homeostasis. KB109 is under evaluation in two COVID-19 clinical studies.

Disclosures

Jeffrey Meisner, PhD, Kaleido Biosciences (Employee, Shareholder) Jackson Lee, PhD, Kaleido Biosciences (Employee, Shareholder) Jonathan Lawrence, PhD, Kaleido Biosciences (Employee, Shareholder) Megan Roed, BA, Kaleido Biosciences (Employee, Shareholder) Johan van Hylckama Vlieg, PhD, Kaleido Biosciences (Employee, Shareholder)
1210. K-mer Profiling Powered by Reference-assisted Assembly of NGS Data: A Highly Sensitive Protocol to Infer the Plasma Microbiome Using Cell-free DNA Sequence Data
Authors: Sinha Rohita , Kleiboeker Steve , Altrich Michelle , Bixler Ellis
Published: January 2021

Background

Cell-free DNA (cfDNA) has emerged as an important clinical specimen to probe for pathogenic microbes, especially in organ transplant patients where the same data can be used to predict allograft rejection. Recent reports described viral, bacterial or the complete microbial diversity in plasma following cfDNA sequencing. The prevalence of certain viral families (anelloviridae) is associated with immunosuppressant dosage and the risk of antibody mediated rejection. While being informative, the cfDNA reads are inherently shorter in length (~160bp or 2x75bp) and predominated by the host DNA (~97-99%), causing challenges in their taxonomic annotation and lower specificity. Here we present a computational protocol which minimizes these challenges by merging the concept of “Reference-assisted Assembly” with K-mer profiles of NGS data, for highly sensitive and specific microbial detection.

Methods

We developed a pipeline in which non-host NGS data (reads not mapped to the human genome) undergo a reference-assisted assembly operation and then taxonomic annotation using KrakenUneq (a K-mer based classifier). We trained the KrakenUneq on an in-house and curated database of ~12,000 viral genomes. We used three different K-mer values (16, 21, 31) to train KrakenUneq, and final predictions are made by applying a majority-wins rule. Currently the default KrakenUneq database is used for bacterial & fungal metagenome analysis. We tested our method on 30 simulated and 124 clinical samples obtained from a biorepository.

Results

Our protocol currently screens for a targeted list of pathogens (15 viral species, 16 bacterial and 10 fungal genera). On a simulated set of viral sample mixes, our protocol had 100% accuracy. For 124 clinical samples, predictions were evaluated for specificity and sensitivity using qPCR assays for the following viral species: EBV, BKV, JCV, HSV1/2, HHV7, and CMV. Total 33/38 computational predictions (87%) were confirmed by qPCR. The prediction sensitivity in terms of cps/ml ranged from 6 - 106 copies/mL.

Conclusion

Our efforts to perform ‘Reference-assisted assembly’ followed by K-mer based taxonomic annotation of cfDNA data, led to development of a novel and accurate pathogen detection protocol.

Disclosures

Rohita Sinha, PhD, Viracor-Eurofins (Employee) Steve Kleiboeker, DVM, PhD, Viracor-Eurofins (Employee) Michelle Altrich, PhD, Viracor-Eurofins (Employee) Ellis Bixler, MS, Viracor-Eurofins (Employee)
1211. Response to Fecal Microbiota Transplant (FMT) in Refractory Clostridioides difficile Infection (CDI) is Modest Compared to Recurrent CDI in Hospitalized Patients
Authors: Shin Jae Hyun , Hays R Ann , Warren Cirle
Published: January 2021

Background

There are limited options for Clostridioides difficile infection (CDI) refractory to conventional antibiotic therapy (metronidazole, vancomycin, or fidaxomicin). Fecal microbiota transplant (FMT) is considered a safe and effective treatment for recurrent CDI but has not been widely utilized for refractory CDI due to concerns about safety. Even when included in studies, refractory CDI has not been analyzed separately from recurrent CDI. We reviewed cases of FMT performed in the inpatient setting for CDI to evaluate its safety and efficacy for refractory CDI.

Methods

Patients who received FMT inpatient at University of Virginia Health System for recurrent or refractory CDI after Infectious Diseases and Gastroenterology consultation signed informed consent acknowledging that FMT was considered investigational use in CDI not responding to standard of care as per 2014 FDA guidance. Charts were reviewed as part of quality improvement efforts to evaluate safety and efficacy of FMT in inpatient setting.

Results

Starting in July 2014, 13 patients received FMT for CDI as inpatients. Six received FMT for recurrent CDI, with four having complete resolution, one had recurrent CDI, and one had persistent C. difficile-negative diarrhea, for cure rate of 83%, comparable to published studies. Seven patients received FMT for refractory CDI, with three resulting in complete resolution. One responded to FMT but refused further care, one died from multiorgan failure after initial response to FMT that was possibly related to CDI, strongyloides, and/or CMV. Two patients had ongoing diarrhea suggestive of post-infectious irritable bowel syndrome, one was C. difficile-negative and one was not tested. The cure rate was 57%, lower than that of the recurrent CDI, but without any clear evidence of microbiologic failure.

Outcome of patients undergoing FMT for CDI in the inpatient setting at University of Virginia Health System

Conclusion

Cure rate for FMT for refractory CDI was lower than recurrent CDI, but review of the cases of treatment failures did not reveal any microbiologic evidence of failure. FMT should be considered an alternative option when treating refractory CDI.

Disclosures

All Authors: No reported disclosures
1212. Temporal Dynamics of the Plasma Microbiome in Recipients at Early Post-liver Transplantation
Authors: Okumura Toshihiko , Horiba Kazuhiro , Kamei Hideya , Takeuchi Suguru , Suzuki Takako , Torii Yuka , Kawada Jun-ichi , Takahashi Yoshiyuki , Ogura Yasuhiro , Ogi Tomoo , Ito Yoshinori
Published: January 2021

Background

Immunosuppression during liver transplantation (LT) enables the prevention and treatment of organ rejection, but poses a risk for severe infectious diseases. Antimicrobials are often required for patients after LT. Recently, the genomes of multiple microorganisms have been detected in blood, which is essentially sterile. Immune modulation and antimicrobials affect the blood microbiome. Thus, determining the impact of immunosuppression and antimicrobials on the microbiome may be important to understand immunocompetence, predict clinical adverse events after LT such as acute cellular rejection (ACR), and treat infectious diseases.

Methods

Fifty-one patients who received LT at Nagoya University Hospital from 2016 to 2018 were enrolled. Plasma samples were retrospectively collected within a week after LT, 4±1 weeks after LT, 8±1 weeks after LT, and within 2 days after a positive blood culture. A total of 111 plasma samples were analyzed using shotgun next-generation sequencing (NGS). Sequence data were imported into the custom-made analysis pipeline PATHDET.

Results

The relative abundance of Anelloviridae, Nocardiaceae, Microbacteriaceae, and Enterobacteriaceae significantly changed during the postoperative period (figure 1). Microbiome diversity was higher within a week after LT than at 8 weeks after LT. Antimicrobials were significantly associated with the microbiome of LT recipients. In addition, the proportion of Enterobacteriaceae was significantly decreased (figure 2) and the plasma microbiome diversity was significantly higher in patients with ACR than in non-ACR patients. Finally, sequencing reads of bacteria isolated from blood cultures were predominantly identified by NGS in 8 of 16 samples (figure 3), and human herpesvirus 6 was detected as a causative pathogen in one recipient with severe infectious diseases.

Change in the relative abundance of each microorganism at the family level of taxonomic hierarchy in plasma samples after liver transplantation

Comparison of the plasma microbiome at the family level in patients with and without acute cellular rejection

Relative abundance of microorganisms at the species level in plasma from patients with positive blood cultures

Conclusion

The metagenomic NGS technique has great potential in revealing the plasma microbiome and is useful as a comprehensive diagnostic procedure in clinical settings. Temporal dynamics of specific microorganisms may be used as indirect markers for the determination of immunocompetence and ACR in LT recipients.

Disclosures

All Authors: No reported disclosures
1214. Clinical characteristics of patients with adrenal insufficiency presenting fever
Authors: Jang wooyoung , Sohn Youngseok , Park Jung Hwan , Kim Bongyoung
Published: January 2021

Background

The aim of the present study is to analyze the clinical characteristics of adrenal insufficiency patients presenting fever.

Methods

A single-center retrospective study was conducted in an 846-bed tertiary hospital in South Korea. All hospitalized adult patients (age ≥19 years) who diagnosed with adrenal insufficiency between March 1, 2018 and June 30, 2019 were recruited. Only the first event per patient was included and patients were excluded if they: (1) had proven structural problems with adrenal or pituitary gland, (2) had a history of chemotherapy within 6 months prior to the diagnosis of adrenal insufficiency, and (3) had other medical conditions which may cause fever.

Results

A total of 150 cases were included: 45 (30.0%) had fever and 105 (70.0%) did not have fever at the time of diagnosis of adrenal insufficiency. The proportion of female patients was lower in patients with fever compared to those without fever (44.4% vs. 67.6%, P =0.008). In addition, patients with fever were diagnosed at 13.98 ± 14.51 days, which was later than 6.47 ± 6.91 of patients without fever (P < 0.001). Higher proportion of patients with fever had history of surgical procedure within 6 months (33.3% vs. 11.4%, P =0.001) and antibiotic usage at the time of diagnosis (80.0% vs. 17.1%, P < 0.001) compared to those without fever. Among clinical manifestations, general weakness (91.1% vs. 66.7%, P =0.002), headache (15.6% vs. 4.8%, P =0.044), and cough (17.8% vs. 4.8%, P = 0.022) were more frequently observed in patients with fever. There were no significant differences in clinical outcomes between two groups. According to the multivariate analysis, female sex (OR =0.32, 95% CI: 0.12–0.86, P = 0.024) lowered the risk for adrenal insufficiency with fever. In comparison, history of surgical procedure within 6 months (OR = 4.35, 95% CI: 1.23–15.39, P =0.023), general weakness (OR = 7.21, 95% CI: 1.71–30.37, P =0.007), and cough (OR = 17.29, 95% CI: 1.09–274.92, P =0.043) were significantly associated with adrenal insufficiency with fever.

Table. Risk factors for adrenal insufficiency with fever using a multivariable logistic regression model

Conclusion

Approximately 30% of adrenal insufficiency presented fever. In patients with adrenal insufficiency and male sex, history of surgical procedure within 6 months, general weakness, and cough may be associated with presenting fever.

Disclosures

All Authors: No reported disclosures
95. Assess reasons for continuing antibiotics in persons with positive respiratory viruses PCR in the emergency room
Authors: kassar rawan , dandukuri nandini , troquet jean- Marc , Frenette Charles
Published: January 2021

Background

Respiratory tract infections remain one of the major reasons for inappropriate antibiotic usage. The multiplex PCR respiratory viral panel improves the diagnostic ability of viral causes of RTI and have been advocated as a useful stewardship tool. We sought to evaluate factors leading to continued antibiotic following a positive respiratory viral PCR and to evaluate the impact of a targeted antimicrobial stewardship intervention on antibiotic use.

Methods

In this Quasi experimental study, adult patients presenting to RVH ER with positive respiratory PCR from January 13 2020 to February 27 2020 were reviewed. Patient demographics, clinical, comorbidities, laboratory and radiology reports, antibiotic and antiviral usage before and after test were recorded. For patients without microbiological or radiological evidence of bacterial infection, a standard questionnaire was administered to treating physician. Antibiotic prescribing rate before and following a positive PCR and antibiotic discontinuation following ASP questionnaire was tracked.

Results

During the study period, 147 adult patients presented to the ER with positive respiratory PCR were. Among the study population, antibiotic prescription rate was 49% prior to test result. Influenza was the most common respiratory virus isolated(89/147). Following the respiratory viral PCR, antibiotics were stopped 39% and continued in 51 % by the treating physician. Main reasons for antibiotic continuation included concurrent bacterial infection16/30 (pneumonia 9/30), COPD exacerbation 5/30, febrile neutropenia (5/30) and hemodynamic instability(4/30). Antibiotics were continued without obvious indications in 15 patients and were targeted for intervention. Overall 66% (10/15) of ASP interventions were accepted and antibiotics discontinued. Overall antibiotics were discontinued in 53 % of patients in whom they were initiated pretest result.

Conclusion

This study shows that positive respiratory virus PCR is very useful as it led to discontinuation of antibiotics by treating physician in 40 % and further 13% by an antibiotic stewardship intervention. Adding a stewardship intervention after test result further adds reduction to antibiotic usage.

Disclosures

All Authors: No reported disclosures
1215. Evaluation of the Carba-R NxG Assay in a Global Challenge Set of Pseudomonas aeruginosa
Authors: Gill Christian M , Asempa Tomefa E , Tickler Isabella A , Cruz Caitlin dela , Tenover Fred C , Nicolau David P
Published: January 2021

Background

Carbapenem-resistant P. aeruginosa (CRPA) is a growing clinical challenge. Carbapenemase production is particularly problematic due to high transmissibility and limited treatment options. Carbapenemase prevalence and diversity are largely driven by geography and thus testing spectrum will dictate utility in certain regions. The purpose of this study was to evaluate the performance of the research-use-only Xpert® Carba-R NxG (Carba-R NxG) and commercially available Xpert® Carba-R (Carba-R) in a global collection of P. aeruginosa.

Methods

The challenge set included 123 clinical P. aeruginosa isolates from 11 countries. Isolates were previously categorized via PCR or whole-genome sequencing. Carbapenemase classes tested include: VIM, IMP, NDM, SPM, KPC, and GES. Non-carbapenemase (non-CP) harboring isolates were also tested (negative control). Isolates were tested using the Carba-R NxG and the Carba-R per manufacturer instructions. Carba-R NxG testing was completed by Cepheid (Sunnyvale, CA) blinded to genotype. Test performances were tabulated for each assay by carbapenemase class.

Results

Both assays gave negative results for all non-CP isolates and positive results for all VIM, NDM, and KPC isolates. An improvement in IMP detection among isolates was observed (Carba-R NxG 100% vs. Carba-R 58% detection). All SPM and GES isolates, targets not present in the current Carba-R, were positive by Carba-R NxG. Two isolates harbored both VIM and GES, while a third isolate contained VIM and NDM. The Carba-R NxG identified both targets in all 3 isolates while the Carba-R was negative for both GES-containing isolates. Table 1 provides the test performance of both assays. Overall, the Carba-R NxG successfully categorized 100% of isolates tested compared with 68% for its predecessor.

Table 1. Test performance of Carba-R NxG and Commercially Available Carba-R by Carbapenemase Class.

Conclusion

As the prevalence and diversity of carbapenemase-producing CRPA continues to expand, the Carba-R offers a rapid and sensitive assay to identify clinically relevant carbapenemase genotypes to inform infection prevention and therapeutic interventions. The Carba-R NxG will expand the current targets including SPM, GES, NMC/IMI, and IMP-subtypes, outside the previous testing spectrum, increasing the global utility of the test.

Disclosures

Isabella A. Tickler, BS, Cepheid (Employee) Caitlin dela Cruz, BS, Cepheid (Employee) Fred C. Tenover, PhD, Cepheid (Employee) David P. Nicolau, PharmD, Cepheid (Other Financial or Material Support, Consultant, speaker bureau member or has received research support.)Merck & Co., Inc. (Consultant, Grant/Research Support, Speaker’s Bureau)Wockhardt (Grant/Research Support)
1216. Benchmarking Published Gene Signatures for Robust Infection Classification
Authors: Bodkin Nicholas , Ross Melissa H , Henao Ricardo , Tsalik Ephraim L
Published: January 2021

Background

Host gene expression has emerged as a promising diagnostic strategy to discriminate bacterial and viral infection. Multiple gene signatures of varying size and complexity have been developed in various clinical populations. However, there has been no systematic comparison of these signatures. It is also unclear how these signatures apply to different clinical populations. This meta-analysis examined 19 published signatures, validated in 49 publicly available datasets for a total of 4750 patients. The objectives were to understand how the signatures compared to each other with respect to composition and performance, and to evaluate their performance in different patient subgroups.

Methods

Signatures were characterized with respect to size, platform, and discovery population. For each of the 19 signatures, we ran leave-one-out cross-validation to generate AUCs for bacterial classification and viral classification. We then applied dataset-specific thresholds to generate accuracies, pooling patients across datasets.

Results

Signature performance varied significantly with a median AUC across all validation datasets ranging from 0.55 to 0.94 for bacterial classification and 0.79 to 0.96 for viral classification. Signature size varied (1- 341 genes) with smaller signatures generally performing more poorly for both bacterial classification (P < .001) and for viral classification (P = 0.02). Viral infection was easier to diagnose than bacterial infection (85% vs. 80% overall accuracy, respectively; P < .001). Host gene expression classifiers performed more poorly in children < 12-years compared to those older than 12-years for both bacterial infection (77% vs. 83%, respectively; P < .001) and for viral infection (82% vs. 89%, respectively; P < .001). We did not observe differences based on illness severity as defined by ICU care for either bacterial or viral infections.

Conclusion

We observed significant differences among gene expression signatures for bacterial/viral discrimination, though these were not due to variations in the discovery methods or populations. Signature size directly correlated with test performance, which was generally better for the diagnosis of viral infection and in populations >12-years.

Disclosures

Ephraim L. Tsalik, MD, MHS, PhD, Predigen (Shareholder, Other Financial or Material Support, Founder)
1218. Comparing the Diagnostic Accuracy of Clinician Judgement to a Novel Host Response Diagnostic for Acute Respiratory Illness
Authors: Jaffe Ian S , Jaehne Anja K , Quackenbush Eugenia , McClain Micah T , Ginsburg Geoffrey S , Woods Christopher W , Rivers Emanuel , Tsalik Ephraim L
Published: January 2021

Background

Discriminating bacterial and viral infections remains clinically challenging. The resulting antibacterial misuse contributes to antimicrobial resistance. Host gene expression-based tests are a promising strategy to discriminate of bacterial and viral infections, but their potential clinical utility has not yet been evaluated.

Methods

A host gene expression biosignature was measured using either qRT-PCR or microarray in 683 ED subjects with suspected infection. Based on chart reviews, we recorded clinical diagnosis as defined both by the provider assessment and by the provider treatment plan. The biosignature, diagnosis, treatment plan, and procalcitonin were compared to clinical adjudication as the reference standard. With this as a baseline, we then calculated average weighted accuracy (AWA) and change in overall net benefit (∆NB), weighting bacterial false negatives four times more seriously than false positives.

Results

Gene expression correctly classified the three possible disease etiologies (bacterial, viral, or non-infectious) 76.1% of the time, outperforming provider diagnosis, provider treatment, and procalcitonin (Table 1). Overall accuracy was higher in subjects with bacterial infections (n=278, 83.8% accurate) compared to those with viral (n=234, 76.5%) and non-infectious (n=171, 63.2%) etiologies. Due to a strong sensitivity bias to treat bacterial infections at the expense of diagnostic accuracy and specificity, the provider diagnosis was overall more accurate than the corresponding treatment plan (71.4% accuracy vs. 68.1%), resulting in inappropriate antibiotic use in 41.0% of cases where antibiotics were prescribed. The gene expression test had significantly higher AWA for the diagnosis of bacterial infection than both procalcitonin and provider treatment (82.4% vs. 70.3% and 74.4%, respectively; p < 0.0001). Consequently, the host gene expression test had greater net benefit than provider treatment (∆NBbact = 9.9%), provider diagnosis (∆NBbact = 4.4%), and procalcitonin (∆NBbact = 27.1%).

Table 1: Summary of provider, procalcitonin, and host gene expression test performance in a cohort of 683 subjects.

Conclusion

Host gene expression-based tests to distinguish bacterial and viral infection can facilitate more appropriate treatment, leading to improved patient outcomes and mitigating the antibiotic resistance crisis.

Disclosures

Geoffrey S. Ginsburg, MD PhD, Predigen, Inc (Shareholder, Other Financial or Material Support) Ephraim L. Tsalik, MD, MHS, PhD, Predigen (Shareholder, Other Financial or Material Support, Founder)
1220. Disruption of the Body Temperature Circadian Rhythm in Hospitalized Patients
Authors: Geneva Ivayla I , Javaid Waleed
Published: January 2021

Background

The circadian rhythm is believed to offer survival advantage with dysregulation being linked to immune response deficiencies and metabolic derangements. Diurnal temperature variation exists in humans, yet its preservation during illness is not well understood. Herein we present an analysis of diurnal body temperatures among hospitalized patients, with a focus on infectious versus non-infectious diagnoses.

Methods

Temperatures measured within 1/2 hour of 8am, 12pm, 4pm, 8pm, 12 am, and 4am from 16,245 hospitalized patients were analyzed using descriptive statistics and t-tests.

Results

Although we found a diurnal pattern when analyzing the ensemble of temperatures from all patients (Figure 1), stratified by measurement site (oral, axillary, temporal, and tympanic), the through-to-peak difference was only 0.2F (0.1C), while previously reported diurnal difference in healthy volunteers was 1.9 °F (1.06 °C). Data from the core body temperature sites monotherm and rectal did not show any diurnal pattern. The peaks in body temperature occurred at 8 pm for all patients, regardless of age, which is similar to healthy people. However, the minimum body temperature was shifted to later times compared with healthy people (6am or 2 hours before rising in health) – for young patients (age 20-30 years, N=1285) the through was at 8am and for elderly patients (age 70-80 years, N=1736), it was at 12pm (Figure 2). Analysis of body temperature of individual patients showed that less than 20% of patients exhibited diurnal variation and among those showing variation, the trend was present only on the minority of hospitalization days (Table 1). Interestingly, the presence or absence of an infectious process did not influence the proportion of patients showing diurnal variation.

Figure 1

Figure 2

Table 1

Conclusion

Hospitalization is associated with disruption in the circadian rhythm as reflected by patients’ body temperature, with shifting of the diurnal variation curve and blunting of the temperature range both in the ensemble and on the individual level. The trend is not influenced by having an infection. However, since core body temperatures tend to be the measurement site of choice in the ICU setting, we suspect that further obliteration of the diurnal rhythm occurs with more severe disease.

Disclosures

All Authors: No reported disclosures
1223. Impact of Helicobacter pylori Infection on Duodenal Microbial Community Structures and Microbial Metabolic Pathways
Authors: Maeda Tadashi , zai hiroaki , Fukui Yuto , katou yoshihumi , kumade eri , watanabe toshiyasu , Furushou Norihiro , Nakajima Hitoshi , arai kazuho , Ishii Yoshikazu , tateda kazuhiro , Urita Yoshihisa
Published: January 2021

Background

Recent reports suggest that Helicobacter pylori infection causes extragastric diseases. However, the onset mechanisms of these diseases have not been fully elucidated, and the factors involved in the onset of these extragastric diseases remain obscure.

Methods

Forty-seven (20 male, 27 female) subjects who underwent gastric cancer screening were enrolled. Aspirated duodenal fluid samples were collected from the descending duodenum. Samples were analyzed by 16S rRNA gene amplicon sequencing to investigate whether the duodenal microbiota and microbial biofunctions were affected by H. pylori infection.

Results

Thirteen subjects were H. pylori positive while 34 were negative. We observed 1404 bacterial operational taxonomic units from 23 phyla and 253 genera. In the H. pylori positive group, we observed higher abundance of Proteobacteria and lower abundance of Actinobacteria and TM7 than in the H. pylori negative group. The abundance of 10 genera differed significantly between the H. pylori positive and negative groups. Aspects of microbiota in the H. pylori positive group were significantly influenced by 12 taxa primarily belonging to Gammaproteobacteria, compared with those in the H. pylori negative group. Microbial functional annotation collated using the Kyoto Encyclopedia of Genes and Genomes Orthology database showed that 12 microbial metabolic pathways were significantly affected by H. pylori infection.

Conclusion

1. pylori infection disrupted the normal bacterial communities in the duodenum and changed aspects of the commensal microbial functions primarily by upregulating the metabolic pathways. This may be one of the principal factors in the development of extragastric diseases.

Disclosures

All Authors: No reported disclosures
1224. Investigation of Infectious Etiologies in the Lower Respiratory Tract from Pediatric Patients with Unexpected Cardiopulmonary Deterioration using Next-Generation Sequencing
Authors: Takeuchi Suguru , Kawada Jun-ichi , Horiba Kazuhiro , yamaguchi Makoto , Okumura Toshihiko , Suzuki Takako , Torii Yuka , Kawabe Shinji , Wada Sho , Ikeyama Takanari , Ito Yoshinori
Published: January 2021

Background

In pediatric patients, unexpected cardiopulmonary deterioration with or without following cardiopulmonary arrest (CPA) are rare events, but can be caused by any of several etiologies, including infectious diseases. The most common cause of out-of-hospital CPA in children ≤12 years old was sudden infant death syndrome (SIDS), whereas infectious diseases were responsible for approximately 10% of the CPA cases. However, the role of infection may have been underestimated as triggers of SIDS or CPA. This study aimed to investigate the infectious etiologies in pediatric patients with unexpected cardiopulmonary deterioration using next-generation sequencing (NGS).

Methods

A total of 16 pediatric patients who were admitted to the pediatric intensive care unit with unexpected cardiopulmonary deterioration with or without following CPA were enrolled. Ten bronchoalveolar fluid (BALF) and six transtracheal aspirates (TTA) samples obtained in the acute phase were used to prepare NGS libraries. The libraries were sequenced on HiSeq and analyzed using metagenome analysis tools.

Results

In ten of 16 patients, one or more bacterial/viral pathogens were detected in the BALF or TTA specimens using NGS. Compared to the conventional culture and viral antigen test results, an additional 6 bacterial (e.g., Chlamydia trachomatis) and 4 viral pathogens (e.g., coxsackievirus A6 and human coronavirus NL63) were identified by NGS in four of ten patients in whom no causative pathogen had been identified by conventional culture and viral antigen tests. A summary of the detected pathogens is listed in Table 1. Notably, sequencing results allowed us to define genotypes for all of the detected viruses in a single NGS assay per patient. Furthermore, based on phylogenetic analysis of the VP1 region, the coxsackievirus A6 strain detected in this study belongs to lineage E2 and harbors an amino acid change (T283A), a substitution that has potential to cause severe illness.

Table 1

Conclusion

Our results suggest that viral and bacterial infection are common triggers in unexpected cardiopulmonary deterioration in pediatric patients. NGS has the potential to contribute to the clarification of the etiology of pediatric critical illness.

Disclosures

All Authors: No reported disclosures
1226. Performance of a Host Response Test for Bacterial/Viral Discrimination in Immunocompromised Patients
Authors: Mahle Rachael E , Suchindran Sunil , Henao Ricardo , Steinbrink Julie M , Burke Thomas W , McClain Micah T , Ginsburg Geoffrey S , Woods Christopher W , Tsalik Ephraim L
Published: January 2021

Background

Difficulty distinguishing bacterial and viral infections contributes to excess antibiotic use. A host response strategy overcomes many limitations of pathogen-based tests, but depends on a functional immune system. This approach may therefore be limited in immunocompromised (IC) hosts. Here, we evaluated a host response test in IC subjects, which has not been extensively studied in this manner.

Methods

An 81-gene signature was measured using qRT-PCR in previously enrolled IC subjects (chemotherapy, solid organ transplant, immunomodulatory agents, AIDS) with confirmed bacterial infection, viral infection, or non-infectious illness (NI). A regularized logistic regression model estimated the likelihood of bacterial, viral, and noninfectious classes. Clinical adjudication was the reference standard.

Results

A host gene expression model trained in a cohort of 136 immunocompetent subjects (43 bacterial, 41 viral, and 52 NI) had an overall accuracy of 84.6% for the diagnosis of bacterial vs. non-bacterial infection and 80.8% for viral vs. non-viral infection. The model was validated in an independent cohort of 134 IC subjects (64 bacterial, 28 viral, 42 NI). The overall accuracy was 73.9% for bacterial infection (p=0.03 vs. training cohort) and 75.4% for viral infection (p=0.27). Test utility could be improved by reporting probability ranges. For example, results divided into probability quartiles would allow the highest quartile to be used to rule in infection and the lowest to rule out infection. For IC subjects in the lowest quartile, the test had 90.1% and 96.4% sensitivity for bacterial and viral infection, respectively. For the highest quartile, the test had 91.4% and 84.0% specificity for bacterial and viral infection, respectively. The type or number of immunocompromising conditions did not impact performance.

Illness Etiology Probabilities

Conclusion

A host gene expression test discriminated bacterial, viral, and non-infectious etiologies at a lower overall accuracy in IC patients compared to immunocompetent patients, though this difference was only significant for bacterial vs non-bacterial disease. With modified interpretive criteria, a host response strategy may offer clinically useful and complementary diagnostic information for IC patients.

Disclosures

Thomas W. Burke, PhD, Predigen, Inc (Consultant) Geoffrey S. Ginsburg, MD PhD, Predigen, Inc (Shareholder, Other Financial or Material Support) Christopher W. Woods, MD, MPH, FIDSA, Predigen, Inc (Shareholder, Other Financial or Material Support) Ephraim L. Tsalik, MD, MHS, PhD, FIDSA, Predigen, Inc (Scientific Research Study Investigator, Shareholder, Other Financial or Material Support)
1228. The Role of Procalcitonin (PCT) and Lactic Acid in Febrile Neutropenic Cancer Patients in an Oncological Emergency Center
Authors: Chaftari Patrick , Chaftari Anne-Marie , Hachem Ray Y , Yeung Sai-ching , dagher Hiba , Jiang Ying , Malek Alexandre , Mulonovich Victor , Raad Issam I , Raad Issam I
Published: January 2021

Background

Procalcitonin (PCT) and lactic acid have emerged as biomarkers that increase in bacterial infections/sepsis and have been used in conjunction with clinical judgment to guide antibiotic administration. The Multinational Association for Supportive Care in Cancer (MASCC) risk index has been used to classify the risk for patients with neutropenic fever. However this index includes subjective elements and complex metrics that make it difficult to use in an oncological emergency center (EC). The purpose of this study is to evaluate the role of serum PCT alone and in combination with lactate to predict bloodstream infections (BSI), hospitalization and 14 days mortality in febrile neutropenic cancer patients presenting to the EC.

Methods

We conducted a retrospective study of all febrile neutropenic cancer patients who presented to our EC between April 1, 2018 and April 30, 2019 and had a serum PCT and lactic acid levels done. Fever was defined either as a documented temperature of ≥100.4 °F or a chief complaint of fever reported at home. Neutropenia was defined as an absolute neutrophil count ≤500 cells/mL.

Results

We included 550 cancer patients of which 385 (70%) had hematologic malignancies and 165 (30%) had solid tumors. A BSI was documented in 116 (21%) patients due to gram negative organisms in 66%, gram positive organisms in 30%, and both in 4%. A higher rate of mortality within 14 days of EC presentation was seen in patients whose PCT ≥ 0.25 compared to those with PCT < 0.25 (5.2% vs 0.7%; p=0.002). Similarly a higher rate of BSI and a longer hospital stay was seen in patients whose PCT ≥ 0.25 compared to those with PCT < 0.25. A PCT ≥ 0.25 or a lactate level >2.2 had a sensitivity of 93% and a negative predictive value of 100% for a 14 day mortality. A logistic regression analysis showed an association between BSI and hematological malignancy, PCT ≥ 0.25, and lacate level >2.2 mmole/L.

Conclusion

A PCT ≥ 0.25 was associated with BSI, LOS and 14 day mortality. The combination of PCT / serum lactate have a good sensitivity and high negative predictive value for BSI and mortality. Because this combination could be useful in identifying the high risk febrile patients requiring hospital admission, it will be compared to the standard but more labor intensive MASCC score index.

Disclosures

Issam I. Raad, MD, Citius (Other Financial or Material Support, Ownership interest)Cook Medical (Grant/Research Support)Inventive Protocol (Other Financial or Material Support, Ownership interest)Novel Anti-Infective Technologies (Shareholder, Other Financial or Material Support, Ownership interest)