bluuebunny/crossref_metadata_2025 huggingface dataset:
417. Factors associated with 30-day Mortality in Carbapenems-resistant Enterobacteriaceae Infections
Authors: Osaithai Naphol , Meesing Atibordee , So-Ngern Apichart
Published: December 2022

Background

Carbapenem-resistant Enterobacteriaceae (CRE) infections are the serious conditions and provide high mortality. The studies of risk factors of death in CRE infection have been limited particularly in our center. Hence, the study was conducted for evaluating mortality and factors associated with CRE infection.

Methods

A retrospective cohort study was conducted between January 1st, 2015, and December 31st, 2019 in sigle center medical university. All patients diagnosed CRE infections who aged ≥ 18 years were included and reviewed. The multivariate logistic regression was used for evaluating the factors associated with 30-day mortality.

Results

Ninety-three patients enrolled in the study. The 30-day mortality occurred in thirty-five patients (37.6%). The non-survive patients had significantly higher simplified acute physiology (SAP) II score, sepsis at the time of diagnosis, and pneumonia (p< 0.05) than survive patients. The most common pathogen was Klebsiella pneumoniae, Escherichia coli and Enterobacter spp. The most common CRE isolates were susceptible to fosfomycin, tigecycline, and colistin (96.7%, 95.7%, 90.3%, respectively). The independent factors associated with 30-day mortality were having simplified acute physiology (SAP) II score > 30 [adjusted odds ratio (aOR) of 12.98 (95% confidence interval (CI), 2.84-59.34, p=0.001)], sepsis at the time of diagnosis [aOR of 4.77 (CI 1.19-19.20, p=0.03)], pneumonia [aOR of 4.64 (CI 1.31-16.47, p=0.01)], and improper empiric antibiotic [aOR of 7.83 (CI 1.84-33.37, p=0.01)].

Conclusion

The mortality of CRE infections were high. The factors associated with 30-day mortality were having SAP II score > 30, sepsis at the time of diagnosis, pneumonia, and improper empiric antibiotic.

Disclosures

All Authors: No reported disclosures.
425. Spread of Carbapenem-resistant Enterobacteriaceae in Intensive Care Unit and effective preventative strategies: Agent-based model study
Authors: Baek Yae Jee , Cho Nathan , Kim Chansoo , Lee Jeehyun , Choi Jun Yong
Published: December 2022

Background

Carbaepenem-resistant Enterbacteriaceae (CRE) could propagate through person-to-person contacts such as contaminated hands of staff, contamination of the environment, or the use of contaminated medical equipment by spreading carbapenemase encoded in plasmid and cause healthcare associated infections (HAIs). Critically ill patients in a compact space of Intensive care unit (ICU) are at significantly high risk of CRE infection, which should be protected by effective infection control strategies. Agent-based model (ABM) has been employed to examine the spread of infectious organisms and estimate the impact of intervention as it reflects behaviors of heterogeneous individuals. We aimed to create an ABM reflecting the medical ICU and identify preventative strategies to reduce CRE infection in the ICU.

Methods

The blueprint of the medical ICU in a tertiary hospital in Republic of Korea was obtained. Researchers had a meeting with the head staffs to get information about healthcare workers (HCWs), patients, and the spatial unit. In this unit, HCWs visiting a patient in ICU are required to wash their hands and wear personal protective equipment. We did a survey to collect data of the routes and the handwashing rates of HCWs. An ABM was made using Python’s Mesa library which simulates the situation in the ICU and the status of CRE. Figure 1.(A) Blueprint of ICU in Severance Hospital, (B) Simulated ICU in agent-based modelFigure 2.Dynamics between agents and environment

Results

Medical ICU consists of two units, and each unit holds fifteen beds. Five nurses work in each unit and six doctors and three technicians take rounds daily, contacting patients in the ICU. The dynamics among agents and environment were constructed.. Parameters were set up from the real world data or the clinical studies. At any given moment, there are about 2.5 patients infected with CRE, and transmission probability and isolation factors were calibrated according to this target. Interventions were enhanced environment cleansing, handwashing of HCWs, and prompt isolation of infected patients through tests and actions. We found those interventions effectively reduced HAIs, and combining effects lead to better results. Figure 3.Parameters and variables in agend-based modelFigure 4.Healthcare associated infections in study periods according to (A) interval of clensing environment, (B) handwashing of HCWs, (C) isolation of infected patients, (D) combined of environmental cleansing and patient isolation

Conclusion

Increasing handwashing rates, environment cleansing, and prompt isolation of infected patients have drastic effects of reducing HAIs caused by CRE in this model, and bundle approach should be considered to prevent the spread of CRE.

Disclosures

All Authors: No reported disclosures.
433. COVID-19 Vaccination Uptake Among Health Care Workers (HCW) Requesting Medical Exemptions to Vaccination.
Authors: Shaw Jana , Brown Loren , Thomas Stephen J , Cleary Lynn M , Bagatell Jarrod
Published: December 2022

Background

New York State adopted a COVID-19 vaccination requirement for all healthcare workers in September 2021, but they allowed medical exemptions. We examined reasons and frequency of medical exemption requests in an academic medical center.

Methods

We conducted active surveillance of all medical exemption requests in a tertiary care academic center in Central NY. Age, gender, reason for request, prior acceptance of other required vaccines, letter of support from employee provider, adjudication of the request, and impact of the decision on COVID-19 vaccine acceptance were collected prospectively since the mandate became effective.

Results

Among 8,776 HCWs, 108 requested medical exemptions, among those 57 (53%) were denied, 39 (36%) were granted temporary exemption, and 12 (11%) were permanent (Table). Females were more likely to request medical exemptions compared to males, 92 (85%) versus 16 (15%), respectively. Overall, 94 (87%) of the HCWs had a letter from their provider in support of their exemption. Nevertheless, only 47% of those qualified for permanent or temporary exemption using CDC guidelines. The most common reasons for requesting exemption included: having natural immunity, receiving monoclonal antibodies, experiencing a common reaction to previous COVID-19 vaccination, and having an underlying medical condition (Figure 1). The majority of individuals who had a request denied or who received a temporary medical exemption were subsequently vaccinated, 63% and 79%, respectively (Figure 2).

Demographic and other characteristics among health care workers (HCW) requesting medical exemptions. Table

Reasons for requesting medical exemption from COVID-19 vaccination requirement by request determination. Figure 1

COVID-19 vaccine uptake among health care workers (HCW) requesting medical exemptions to COVID-19 vaccination. *One HCW received alternative COVID-19 vaccine. Figure 2

Conclusion

Females were more likely to request a medical exemption to vaccination and their requests were often supported by their providers. Future efforts should focus on educating both health care providers and the public about actual medical contraindications or precautions to vaccination to improve overall vaccination rates.

Disclosures

Jana Shaw, MD,MS,MPH, Pfizer: Advisor/Consultant Stephen J. Thomas, MD, Clover: case adjudication committee (compensated for time)|EdJen: Advisor/Consultant|Icosavax: data monitoring (compensated for time)|Island Pharma: Ownership Interest|Merck: Advisor/Consultant|Moderna: chair, safety monitoring committee (compensated for time)|New Day Diagnostics: Honoraria|Pfizer: Advisor/Consultant|PrimeVax: Ownership Interest|Sanofi Pasteur: Advisor/Consultant|Takeda: Advisor/Consultant|Takeda: case adjudication committee (compensated for time)|Vaxxinity: data monitoring committee (compensated for time).
467. Antifungal Therapy in Candida Intra-abdominal Infections Following Source Control
Authors: Buck Margaret , Carr Dustin R , Bremmer Derek N , Jenniches Daniel , Babowice James , Chung Eunice L
Published: December 2022

Background

Current literature suggests that many surgical patients with Candida isolated from an intra-abdominal source do not develop symptomatic infections, however, Infectious Disease Society of America (IDSA) Guidelines recommend antifungal treatment in Candida intra-abdominal infections. An article published by Fabre et al found similar incidence of treatment failure between patients appropriately treated for Enterococcus intra-abdominal infections compared to patients without Enterococcus coverage following source control. Enterococcus and Candida are both low-virulent microorganisms, questioning the necessity of antifungal therapy following source control in Candida intra-abdominal infections.

Methods

This was a retrospective, cohort study of adult patients with intra-abdominal infections who underwent source control and isolation of Candida in intra-abdominal cultures. Eligible patients were separated based on receipt of antifungals. Patients were excluded if they received between 24 hours and 3 days of antifungal therapy, had candidemia prior to intervention, or received prophylactic or therapeutic antifungals within 7 days of intervention. The antifungal group and non-antifungal group were assessed for incidence of treatment failure, defined as death or additional unplanned surgical or antimicrobial interventions for intra-abdominal infections.

Results

A total of 125 patients were included with 77 patients (61.6%) receiving antifungal therapy and 48 patients (38.4%) not receiving antifungal therapy. Patients who received antifungal therapy had a higher median SAPS II score (29 vs 22.5; p = 0.003). There was no difference in the incidence of treatment failure at 30 days between the antifungal and non-antifungal groups (41.6% and 35.2%, respectively; p = 0.62). Median hospital length of stay (14 vs 8.5 days; p < 0.001) and median total duration of antimicrobial therapy (10 vs 7 days; p = 0.667) was longer in the antifungal group compared to the non-antifungal group, respectively.

Conclusion

Patients with Candida intra-abdominal infections that underwent source control had a similar rate of treatment failure at 30 days regardless of receipt of antifungal therapy. However, those who received antifungal therapy had a higher severity of illness.

Disclosures

Dustin R. Carr, PharmD, BCPS, BCIDP, Merck: Honoraria Derek N. Bremmer, PharmD, BCPS-AQ ID, Thermo Fisher Scientific: Honoraria.
479. Predisposing factors and outcomes of infections due to rare yeasts: a study from an apex medical center in India (2018-2020).
Authors: Singh Gagandeep , Xess Immaculata , Chowdhury Souradeep , Soneja Manish , Sachdev Janya , Iram Azka
Published: December 2022

Background

Fungi are ubiquitous in the environment, and for patients with risk factors, they can present as pathogens. Unusual fungi often pose a diagnostic challenge and when encountered in practice, albeit infrequently, can delay diagnosis and treatment.

Methods

Over a period of three years (2018-2020), such cases were followed up till death or discharge and all details were noted down. All patients were diagnosed to have invasive fungal disease according to the EORTC/MSG criteria. Species identification was performed using MALDI-TOF MS and antifungal susceptibility testing (AFST) was done using standard CLSI guidelines.

Results

A total of 14 cases of rare yeasts were noted out of a total of 155 infections due to yeasts. Among these 5 presented with fungemia and 9 with invasive fungal infections (IFI). Of the IFI clinical isolates, there were 2 pus samples and 7 sterile fluids. The majority of these 14 patients were male (11) and belonged to extremes of age (8). The risk factors included CKD (2), prior history of tuberculosis (2), CLD (1), congenital heart disease (2), and type 2 diabetes mellitus (1). Pathogens isolated were Candida guilliermondii (2), Candida pelliculosa (2), Lodderomyces elongisporus (1) from the blood samples, and Trichosporon asahii (6), Candida guilliermondii (1), Candida kefyr (1), and Geotrichum spp. (1) from the other samples. Certain Candida species showed higher MICs to azoles and echinocandins. Trichosporon and Geotrichum showed higher MICs to azoles.

Unfortunately, half of the patients (7) received no antifungals. Of those who did, 4 received mono therapy with azoles or Amphotericin B, while other 3 received combination or sequential therapy with azoles, echinocandins and Amphotericin B. Of the 14 patients, 3 patients expired. The etiological agents in these cases were Candida pelliculosa (fungemia) and Trichosporon asahii (IFI, 2 cases).

Conclusion

This study aims to highlight the clinical presentation of uncommon yeasts, presenting both as bloodstream infections (BSI) and as invasive disease. Improved methods of detection will help us improve our diagnostic accuracy of uncommon pathogens. The clinician should liaise closely with the laboratory, and treatment should be instituted according to the AFST data.

Disclosures

All Authors: No reported disclosures.
480. Redefining the Epidemiologic Profile of Histoplasmosis from 2011 to 2021 in Central Ohio
Authors: Hofmann JustIn , Sobhanie Mohammad Mahdee , Doctor Medical , Sarwar Sajed , Hebert Courtney
Published: December 2022

Background

Histoplasma is a common endemic mycosis in multiple Midwestern states. Most of the data defining epidemiologic risk are from 20th century outbreak investigations. A known exacerbating factor is immune suppression; but use of biologics, immunosuppressants (ISP), and chemotherapy has advanced since these investigations were conducted. This study sought to use clinical data from a tertiary care facility to address these gaps to define the evolving epidemiology of histoplasmosis in Ohio.

Methods

In a single-center retrospective cohort study, we identified adult patients with a histoplasmosis-specific diagnosis, a positive diagnostic test, and an itraconazole/amphotericin B prescription between 1/1/2012 and 10/1/2021. Prisoners were excluded. A random sample of 100 patients underwent in-depth chart review. Comorbidities, environmental risk factors, and ISP use data were collected. Cases were classified by the CDC 2017 Histoplasmosis case definition. “Confirmed” cases had culture growth, a confirmatory lab result, or histopathology plus signs and symptoms of disease, and “probable” cases had a non-confirmatory lab result plus signs and symptoms. Associations between variables were assessed using Fisher’s exact test, p < 0.05.

Results

Of 100 patients, 56 had confirmed and 22 had probable histoplasmosis (Table 1). Three had confirmed blastomycosis, 15 met definitions for both histoplasmosis and blastomycosis, and 4 met neither definition. These were excluded from analysis. No environmental exposure history was documented for 23 of 78 (29.4%) patients. Of those with documented history, 15 (27.1%) had recent renovation or construction exposure; 14 (25.4%) to soil, gardening, or outdoors; 12 (21.8%) to birds, bats, and farm animals; and 25 (45.4%) had no known exposure. There were 51 (65.4%) exposed to at least one dose of ISP in the year prior to diagnosis, including 41 (52.5%) to corticosteroids. Table 1Characteristics of patient cohort

Conclusion

In this cohort, more patients with confirmed or probable histoplasmosis were exposed to ISP than had a documented traditional environmental risk factor. This study shows reliance on traditional environmental exposure history might not accurately gauge risk. Further work is needed using ISP exposure to drive appropriate diagnostic testing.

Disclosures

All Authors: No reported disclosures.
482. The modern face of esophageal candidiasis (EC) in an oncology center: Analysis of 323 cancer patients with EC
Authors: Matsuo Takahiro , Singh Ben S , Wurster Sebastian , Jiang Ying , Bhutani Manoop S , Kontoyiannis Dimiitrios P
Published: December 2022

Background

Historically, EC had been a common infection in the pre-azole era, and it was associated with thrush, cytopenia, chemotherapy, and debility in patients (pts) with malignancy. However, the presentation and outcomes of EC in cancer pts in the current era of new cancer treatments and frequent use of azoles as antifungal prophylaxis are scarcely studied.

Methods

We retrospectively reviewed the risk factors, clinical and laboratory features, and outcome of pathology-documented EC in pts at MD Anderson Cancer Center from January 2017 to October 2021. We followed established criteria for the endoscopy grade of EC (B E Kodsi, et al. Gastroenterology. 1976;71(5):715-9). We used a binary multivariable logistic regression model to determine independent risk factors for treatment failure (defined as relapse within 1 year from EC diagnosis) among pts who received fluconazole for EC treatment.

Results

Among 323 pts with EC, 290 pts (90%) had solid tumors; only 33 pts (10 %) had hematological malignancies. Only 7 (2%) of pts had prior antifungal prophylaxis Esophageal cancer was most common (35%), followed by lung cancer (10.8%), gastric cancer (10.2%), and colon cancer (5.9%). 229 pts (71%) received chemotherapy within 30 days prior to EC diagnosis. The most common symptoms were dysphagia (39%), nausea (20%), and odynophagia (15%); 33% of EC pts were asymptomatic. Oral thrush (2%) was uncommon. Most patients (83%) had non-ulcerative EC (endoscopic grade 1-2), 13% had grade 3, and 4% had grade 4 EC. 206 pts (64%) received antifungal treatment (oral fluconazole in 202). Among pts treated with fluconazole, 27 (13%) had treatment failure. Underlying esophageal disease was the only independent predictor of fluconazole treatment failure on multivariate analysis (adjusted odds ratio 3.88, 95%CI 1.49-10.1).

Conclusion

In a large cohort of 323 contemporary pts with EC the entity is predominantly encountered in pts with solid tumor on no antifungal prophylaxis, especially the ones with underlying esophageal pathology which is a predictor of azole treatment failure. Concomitant thrush was uncommon, and in 1/3 of pts EC was only an endoscopic finding.

Disclosures

Dimiitrios P. Kontoyiannis, MD, ScD, PhD (hon), AbbVie: Advisor/Consultant|Astellas Pharma: Advisor/Consultant|Astellas Pharma: Grant/Research Support|Astellas Pharma: Honoraria|Cidara Therapeutics: Advisor/Consultant|Gilead Sciences: Advisor/Consultant|Gilead Sciences: Grant/Research Support|Gilead Sciences: Honoraria|Merck: Advisor/Consultant.
486. A/California/07/2009-pdm-like (H1N1) Influenza Virus Controlled Human Infection Model (CHIM) Activates Various Immune Cells Despite Induction of Mild Symptomatology
Authors: Toapanta Franklin R , Bernal Paula , Hu Jingping , Roberts Paul C , Luke Catherine J , Makhene Mamodikoe K , Ortiz Justin , Neuzil Kathleen , Sztein Marcelo
Published: December 2022

Background

Influenza vaccines require yearly updates due to constant antigenic drift. Improvement of current vaccines requires a deep understanding of the pathogen as well as immunity to the virus. Controlled Human Infection Models (CHIM) provide opportunities to i) test new vaccine approaches in a controlled environment and, ii) better understand host immunity. The University of Maryland School of Medicine (UMSOM) was one of four clinical sites to conduct an H1N1 influenza A virus (IAV) (A/California/07/2009-pdm-like) challenge in 2019.

Methods

Healthy adult volunteers were intranasally challenged with IAV (2 mL of ∼5x10e6 TCID50/mL). After challenge (Day 1), volunteers were assessed for the development of clinical symptoms, virus shedding, development of anti-influenza antibodies (reported elsewhere). Blood specimens were collected at Days -2, 4, 6, 8, 15 and 61 to assess changes in cellular immunity (flow cytometry and ELISpot). Our sub-study included subjects (n=20) from the UMSOM cohort only.

Results

B cell compartment, ASC (plasmablast) responses to homologous hemagglutinin (HA) and neuraminidase (NA) peaked at Day 8. Anti-HA IgG and IgA ASC responses were present in 95% and 75% participants, respectively. NA IgG and IgA ASC responses were present in 60% and 50% of participants, respectively. In the innate compartment, plasmocytoid dendritic cells (pDCs) as well as Classical (CM), intermediate (IM) and non-classical (NCM) monocytes increased in frequency at various timepoints post-challenge. Myeloid DC (mDC), pDC, CM and IM also upregulated expression of CD38 and/or HLA-DR at specific timepoints. The frequency of the CD16+CD56+ natural killer (NK) cell subset and NKT cells were also increased post-challenge. Among T cells, CD4 and CD8 T effector memory (TEM) and TEM CD45RA+ (TEMRA) were activated (CD38+ HLA-DR+) after challenge (Figure 1). CD4 T follicular helper cells (TFH)-17, TFH-1 and TFH-2 were activated (CD38+ ICOS+) at various timepoints post-challenge. Figure 1.Overview of cellular responses to Influenza CHIM.

The heat maps show changes in population frequency and/or expression of activation markers in innate (DC and monocytes) and T cells after challenge (D-2 pre-challenge). Each square displays the mean (n=20) of the population/marker. The color scale indicates the degree of change.

Conclusion

After influenza CHIM, all cell populations assessed showed signs of activation at diverse time-points. The relationship between the presence of pre-existing protective immunity (HAI >40) and degree of immune activation is still under analysis.

Disclosures

Catherine J. Luke, Ph.D., GSK: Spouse is an employee of GSK Justin Ortiz, MD, Moderna: Advisor/Consultant|Pfizer: Advisor/Consultant.
493. Defining background shared antibody sequences between unrelated healthy individuals (public clonotypes) to support future studies on specific infectious disease related conditions.
Authors: Chang Arthur , Hicar Mark D
Published: December 2022

Background

Public clonotypes, antibodies against specific antigens in unrelated individuals that have genetic similarities, have been shown in a variety of infections, including SARS-CoV-2 and HIV. Likely, there are shared antibody responses between individuals for many infections. To explore antibody responses that would coincide with specific infectious diseases that may set off chronic illnesses, such as Multiple Sclerosis or Alzheimer's disease, defining the background shared clonotypes is needed to differentiate disease from normal background public clonotype responses.

Methods

Heavy chain variable sequences were retrieved from public biorepositories (Bioproject PRJNA486667) composed of 43 healthy persons, and two groups of HIV infected persons; 114 with broadly neutralizing antibodies and 91 without broadly neutralizing antibodies. We utilized the Immcantation package of software run on our SUNY Buffalo computational cluster. After PRESTo annotation, duplicate sequences were collapsed and sequences of only single counts were removed. Clonal groups were determined using ChangeO requiring IGHV, IGHJ, and CDR3 amino acid sequence to be perfectly matched. Figures and statistics were generated with immcantation, excel, and graphpad prism 8.

Results

244850 heavy chain sequences from 43 healthy controls were compared for exact matches to predicted germline variable segment and CDR3 amino acid sequence and identified 0.23% as public clonotypes. Comparison to 205 HIV + individuals (a total of 1.4 million comparative sequences) showed that 2.35% of heavy chain sequences were seen in more than one individual. Generally, public clonotypes had shorter CDR3s (peak of 9 amino acids). VH 3-9, 3-30 and 4-34 were the most commonly used variable segments in public clonotypes. Common exact match CDR3 sequences using a variety of variable sequences, including an 11 amino acid CDR3 sequence motif, were also discovered.

Conclusion

This early work has identified several public clonotypes that are shared among subjects who are HIV positive and otherwise healthy people. Defining the sequences commonly seen between individuals can assist in specifying antibody responses specific to disease states from larger sequence databases.

Disclosures

All Authors: No reported disclosures.
505. Mucosal and Systemic Humoral Immunity Differences between Sexes during Influenza Vaccination and Viral Challenge
Authors: Giurgea Luca T , Bean Rachel , Han Alison , Czajkowski Lindsay , Cervantes-Medina Adriana , Gouzoulis Monica , Baus Holly Ann , Reed Susan M , Athota Rani , Mateja Allyson , Hunsberger Sally , Kash John , Taubenberger Jeffery , Memoli Matthew J
Published: December 2022

Background

In previous influenza challenge studies we observed that the incidence of influenza symptoms was higher in women than in men, and that women experience more symptoms overall. Women also demonstrated lower neuraminidase (NA) inhibition (NAI) antibody titers than men after challenge and regression analysis suggested that NAI titers predict clinical outcomes. We sought to evaluate this using data from a more recent challenge study with more immunologically varied volunteers, while also assessing mucosal immunity.

Methods

We obtained mucosal and serum samples from healthy adults. Half underwent intramuscular quadrivalent influenza vaccination followed by influenza A (H1N1) intranasal challenge while others just challenge alone. Antibody titers and clinical outcomes between sexes were compared.

Results

No significant differences in shedding or symptom outcomes were observed between sexes. Similarly, no differences in systemic titers against NA or hemagglutinin (HA) were seen. Serum total IgG and IgA were also similar between sexes. Prior to vaccination, mucosal IgA titers were significantly lower against HA stalk and NA in women, but these differences disappeared after vaccination. In the unvaccinated group, lower nasal IgA titers were also seen in women pre-challenge. At 7 days post-challenge, differences in mucosal titers between sexes disappeared. However, at 56 days post-challenge, mucosal IgA titers against HA, HA stalk, and NA were all significantly lower in women.

Conclusion

In contrast to our previous findings, no differences in clinical outcomes or systemic NAI titers were observed between men and women, possibly due to differences in underlying immunity between study populations or the lower sample size in this study. However, mucosal differences were noted with women having lower mucosal titers than men against HA stalk and NA at baseline. While influenza vaccination and challenge eliminated differences in the short term, they reappeared 8 weeks after challenge, with all nasal IgA antibody titers (HA, HA stalk, and NA) lower in women. Further studies are necessary to understand the differences in influenza disease and immunity between sexes.

Disclosures

All Authors: No reported disclosures.
525. A Universal ‘Day Zero’ Infectious Disease Testing Strategy Exploiting Crispr-Based Sample Depletion And Metagenomic Sequencing
Authors: Brown Keith
Published: December 2022

Background

The lack of preparedness for detecting the highly infectious SARS-CoV-2 pathogen — the pathogen responsible for the COVID-19 disease — caused enormous harm to the public health, the economy and society as a whole. It took ∼60 days for the first RT-PCR tests for SARS-CoV-2 infection developed by the United States Centers for Disease Control (CDC) to be made available. It then took >270 days to deploy 800,000 of these tests at a time when the estimated actual testing needs required over 6 million tests per day. Testing was therefore limited to only individuals with symptoms or individuals in close contact with confirmed positive cases. Testing strategies that can be deployed on a population scale at ‘day zero’ (i.e., at the time of the first reported case) are needed. Next Generation Sequencing (NGS) has such day zero capabilities with the potential to enable feasible and broad large-scale testing strategies, however it has limited detection sensitivity for low copy numbers of pathogens which may be present. Here we demonstrate that using CRISPR-Cas9 to remove abundant sequences that do not contribute to pathogen detection, NGS detection sensitivity is equivalent to RT-PCR. In addition, we show that this assay can be used for variant strain typing, co-infection detection, and individual human host response assessment – all in a single workflow using existing open-source analysis pipelines. This NGS workflow is pathogen agnostic, and therefore has the potential to radically transform how both very large-scale pandemic response and focused clinical infectious disease testing are pursued in the future.

microbial composition at two test sites

Detection Sensitivity

Methods

Covid positive samples with RT-PCR Ct values from 16-39 were processed through the CRISRP enhanced mNGS pipeline.

Data processing workflow

Results

Sn/Sp compared to RT-PCR was 97%/100%. Strain calling concordance compared to amplicon sequencing was 100%. Co-infections from Covid positive samples were identified with high confidence. Host response signatures match the published literature.

Conclusion

Applying CRISPR enhanced metagenomic NGS at Day Zero of the next pandemic can mitigate the time gap in developing approved diagnostics at population scale and potentially save lives.

Disclosures

All Authors: No reported disclosures.
528. Bacterial vs viral etiology of fever: a prospective study to estimate a host score’s potential to support ED physicians' etiologic accuracy
Authors: Mor Meirav , Paz Meital , Amir Lisa , Levy Itzhak , Scheuerman Oded , Livni Gilat , Guetta-Oz Claire , Yochpaz Sivan , Berant Ron , Schwartz Rama , Niv Omer , Singer Dana , Ashkenazi Shai , Waisman Yehezkel
Published: December 2022

Background

A host-protein score (BV) combining the circulating levels of TRAIL, IP-10 and CRP was developed for distinguishing bacterial from viral infection. BV’s potential to impact decision making at the emergency department (ED) was assessed by comparing BV to physician’s etiological suspicion.

Methods

Rosetta study participants, aged 3 months to 18 years with febrile respiratory tract infection or fever without source, were prospectively recruited in a tertiary care pediatric ED. The main eligibility criteria were symptoms for less than 7 days and immunocompetence. ED physician’s initial etiological suspicion (bacterial/viral/I don’t know) and degree of confidence (low/medium/high) were recorded in a questionnaire. BV was interpreted based on pre-defined score thresholds (viral/bacterial/equivocal); the results were not available to the physician. The etiologic reference standard was based on the diagnoses (bacterial/viral/indeterminate) of 3 independent pediatricians who were provided with all available patient data but blinded to BV. BV’s potential to impact the physician’s etiologic accuracy was estimated according to alignment between BV and etiological suspicion as filled in the questionnaire (assuming full adoption of BV by the physician).

Results

Among 348 patients recruited, 290 met eligibility criteria and had requisite serum sample (Figure 1A). Median age was 1.3 years (interquartile range 1.7), 37.5% were female. 211 patients had questionnaires filled. BV matched physician’s label and reference standard in 72% of the cases (151/211; Figure 1B); of these, 52% (78/151) were labeled by the physician with low/medium confidence, i.e., BV could reinforce the physician’s suspicion. In 12% of the cases (26/211) BV aligned with the reference standard but not with the physician’s suspicion, and therefore could correct the physician's etiologic diagnosis. BV did not align with the reference standard in 7% of the cases (14/211) and was equivocal in 9% of the cases (20/211). Overall, BV could potentially correct physician diagnosis and reduce error >2-fold, from 16.1% to 8.1%. Figure 1.Assessing the potential impact of BV on ED physician’s etiologic accuracy.

(A) Reference standard outcomes and BV scores. (B) BV versus adjudication-based reference standard and ED physician etiologic suspicion. Cases with missing questionnaire were omitted; n=211.

Conclusion

BV has potential to aid the diagnostic process. Future studies are warranted to assess the real-world impact of BV on ED practice.

Disclosures

Meital Paz, MD, MeMed: employee Oded Scheuerman, MD, MeMed: Grant/Research Support Ron Berant, MD, GE: Advisor/Consultant.
548. Target Enriched NGS Reveals Wide Breadth of Viruses Causing Acute Undifferentiated Fever in Thailand
Authors: Yamaguchi Julie , Berg Michael G , Phoompoung Pakpoom , Malinauskas Jenna , Cloherty Gavin , Suputtamongkol Yupin
Published: December 2022

Background

Despite extensive laboratory testing, infectious agents were not detected in approximately 50% of patients hospitalized for acute undifferentiated febrile illnesses (AUFI) at Siriraj Hospital, Bangkok, Thailand. Unbiased Metagenomic Next Generation Sequencing (mNGS) enables detection of any microbe present in patient samples. Target enrichment for viruses represents a highly sensitive and cost-effective approach for overcoming host background in clinical specimens. Plasma collected from 800 patients with undiagnosed AUFI between 2013-2020 were analyzed by mNGS coupled to target enrichment to identify known and novel viruses.

Methods

Plasma was pre-treated with benzonase before extraction on an Abbott m2000 instrument. mNGS libraries were prepared from double-stranded cDNA with Illumina Nextera XT reagents on an epMotion then combined in pools of 24 and hybridized to Comprehensive Viral Research Panel (CVRP; Twist Biosciences) probes covering >15,000 strains of vertebrate viruses. Captured viral sequences were amplified, quantified, and sequenced together on a MiSeq. Reads were taxonomically classified by the SURPI pipeline and aligned in CLC Bio Genomics Workbench software.

Results

CVRP method optimization enabled sequencing of 24-48 libraries per MiSeq run, for which >50% genome coverage was obtained with model viruses spiked into clinical specimens at 1000 cp/ml. This approach revealed an array of >24 different viruses found in 26% of samples. Dengue was the most prevalent at 7.4%, with all four genotypes detected. Other common causes of AUFI such as Chikungunya, HIV-1, HAV, HBV, HCV, and CMV were present in 1.5-2.5% of cases. Less prevalent (< 1%) infections included HEV, HSV-2, EBV, HHV-6, Enterovirus B&D and Parvovirus B19. We also encountered sporadic cases of Measles, Cardiovirus, West Nile, Rotavirus, Picobirnavirus, Polyomavirus 4&5, Kubovirus, and Rabies lyssavirus.

Conclusion

Target capture successfully demonstrated that viruses were important etiologies for unresolved cases of AUFI in Thailand. This data has led to a better understanding of the epidemiology of this clinical syndrome and has implications for proper management of AUFI, including lower rates of unnecessary testing and antimicrobial use.

Disclosures

Julie Yamaguchi, BS, Abbott Labs: Employee Michael G. Berg, PhD, Abbott Labs: Employee Pakpoom Phoompoung, MD, Abbott Labs: Grant/Research Support|Abbott Labs: Employee Jenna Malinauskas, MS, Abbott Labs: Employee Gavin Cloherty, PhD, Abbott: Employee|Abbott: Stocks/Bonds|Abbott Labs: Employee Yupin Suputtamongkol, MD, Abbott Labs: Grant/Research Support.
556. Evaluation of Antimicrobial Susceptibility Patterns Following Implementation of Levofloxacin Prophylaxis in those with Cancer and Blood Disorders
Authors: MacBrayne Christine , Dowell Elaine , Weber Matthew J , Janelle Sarah J , Parker Sarah K
Published: December 2022

Background

Prophylaxis with levofloxacin to prevent bacteremia in certain high-risk oncologic populations has been standard of care since the 2018 publication from the Children’s Oncology Group (JAMA 2018; 320(10)). This study only had susceptibility data for a minority of isolates and did not assess unit-wide impact on development of resistance, an important outcome given fluoroquinolones (FLQs) lead to resistance not only to FLQs but other drug classes, and not only for patients receiving fluoroquinolones rather unit wide. Our objective was to evaluate the development of resistance unit wide after implementing FLQ prophylaxis in our high-risk oncology patients, in addition to evaluating the overall impact on bacteremia.

Methods

A 6-year (1/2016-12/2021) single-center, retrospective review rates of bacteremia and susceptibility data from the Children’s Hospital Colorado Center for Cancer and Blood Disorders, encompassing the FLQ prophylaxis initiation date of 11/2018. All positive blood cultures were extracted from Meditech® or EPIC Beaker®, and susceptibility data from Microscan® or Sensititer®, with Institutional review board approval. Repeat cultures were not included. All data was analyzed using descriptive statistics performed in Excel®.

Results

Within the defined study period, there were 199 total blood cultures. These data were normalized per 1000 central line days, and analysis suggests there has been no significant change in bacteremia rates after implementing levofloxacin prophylaxis. Organisms reported nonsusceptible to levofloxacin or ciprofloxacin rose from over 11% in 2016 to almost 46% in 2021. Comparison of trends before and after the 2018 change reveals a significant difference in percent nonsusceptibility for those antibiotics (p = 0.02). Ceftriaxone or cefotaxime and cefepime were also analyzed and while not statistically significant there was a trend toward increasing resistance for ceftriaxone or cefotaxime (Figures).

Conclusion

Bacteremia on the oncology unit did not decrease after the implementation FLQ prophylaxis in November 2018. Additionally, resistance to FLQ and other antimicrobial classes is increasing, calling into question the benefit of this practice.

Disclosures

All Authors: No reported disclosures.
560. Meningitis/encephalitis PCR panel result and antimicrobial use in children
Authors: Olson Jared , Valentine Marilyn E , Thorell Emily A , Stallsmith Jena , Blaschke Anne J
Published: December 2022

Background

The meningitis/encephalitis multiplex polymerase chain reaction panel (ME PCR) detects common pathogens associated with community acquired CNS infections. The impact of this test on antimicrobial use in children is not well characterized.

Methods

We performed a retrospective, observational study in children < 18 years of age who had ME PCR performed on CSF collected within 24 hours of admission to the hospital, presentation to the ED, or outpatient encounter from January 2018 to April 2022. Decision to order ME PCR was determined by the treating team. There are no restrictions on ordering ME PCR at our institution. The total calendar days of antimicrobial use from 24 hours prior to CSF collection to 7 days after CSF collection was evaluated. Our primary objective was to compare antimicrobial duration between subgroups based on ME PCR results: negative, virus positive, bacteria positive, and positive for both.

Results

Of 1282 ME PCR tests performed, 806 were done within the first 24 hours of the encounter. 190 (23.6%) patients never received antimicrobials for empiric treatment of meningitis/encephalitis and were excluded from subsequent analyses. Demographics and antimicrobial use are summarized for patients receiving at least one dose of an antimicrobial in Tables 1 and 2. CSF WBC was highest in bacteria positive CSF (p< 0.001) followed by viral positive (p=0.0066). A positive bacterial result was associated with a longer duration of ceftriaxone, vancomycin and penicillin G and a shorter duration of acyclovir compared to viral and negative results (Table 2). A positive viral result was associated with a shorter length of total antimicrobial treatment (LOT) than negative (p=0.041) and bacterial positive (p< 0.001).

Conclusion

Positive ME PCR results for bacteria may promote faster initiation of targeted therapy. Positive viral tests were associated with shorter LOT than both negative and bacteria positive ME PCR. Median LOT for negative testing was still 2 days suggesting rapid negative testing does not impact LOT. Prioritizing ME PCR for use in CSF samples with high pretest probability of a positive test may increase its effect on antimicrobial use.

Disclosures

Anne J. Blaschke, MD, PhD, BioFire Diagnostics/Biomerieux: Advisor/Consultant|BioFire Diagnostics/Biomerieux: Grant/Research Support|BioFire Diagnostics/Biomerieux: IP licensed to BioFire Diagnostics through the University of Utah and royalties received through the University of Utah related to the FilmArray|Merck: Advisor/Consultant.
576. Burden of Pneumococcal Disease Due to Serotypes Covered by the 13-Valent and New Higher-Valent Pneumococcal Conjugate Vaccines in All Children and Children at Risk in the United States
Authors: Huang Liping , Cane Alejandro D , Perdrizet Johnna , Arguedas Adriano
Published: December 2022

Background

Routine vaccination with 13-valent pneumococcal conjugate vaccine (PCV13) in infants along with a catch-up option with PCV13/PPSV23 in children with underlying medical conditions (UMC) have considerably reduced invasive pneumococcal disease (IPD) and non-invasive pneumococcal disease (PD), including community acquired pneumonia (CAP) and acute otitis media (AOM), in the United State (US). However, a rise in IPD and non-invasive PD caused by non-PCV13 serotypes has been observed. A 15-valent PCV (PCV15) and 20-valent PCV (PCV20), containing additional serotypes to PCV13, are anticipated for children soon. The objective of the study was to estimate the annual cases, deaths, and economic burden of disease attributable to PCV13, PCV15, and PCV20 serotypes in children < 18 years old overall and those with UMC in the US.

Methods

Estimated annual cases, deaths and direct medical costs associated with PD caused by PCV13, PCV15 and PCV20 serotypes were calculated based on published incidence rates of IPD, CAP, and AOM, along with age-group specific serotype coverage, case fatality rates, and disease-related costs (Table 1). The PD burden in those with UMC were extrapolated based on incidence rate ratios of those with UMC vs. those without UMC. The results were reported for 0-17 years and were further stratified into 2 age groups: 0-4 and 5-17 years. Table 1:Source Data for the Calculation

Results

The estimated annual PD cases attributable to PCV13, PCV15, and PCV20 serotypes in those 0-17 years were 768,301, 1,275,187, and 1,656,716 and in those with UMC were 23,209, 43,579, 63,949 (Table 2.1), respectively. The estimated direct medical costs were $494, $833, $1,103 million in those 0-17 years, and $76, $127, and $186 million in those with UMC, respectively (Table 3.1). The total estimated IPD cases in children with UMC were 18% (PCV13), 20% (PCV15) and 23% (PCV20) of all estimated IPD cases in all children.

Conclusion

This study demonstrates that the clinical and economic burden associated with new serotypes included in higher valent PCVs are substantial and higher in children with UMCs. The result shows that PCV20 will offer broader PCV coverage in the prevention of PD in ages < 18 years overall and those specifically with UMC.

Disclosures

Alejandro D. Cane, MD, PhD, Pfizer: Full time employee|Pfizer: Stocks/Bonds Johnna Perdrizet, MPH, Pfizer Inc: Employee|Pfizer Inc: Stocks/Bonds Adriano Arguedas, Medical director, Pfizer: Stocks/Bonds.
577. Cord Blood Protective Antibodies Seroprevalence against Diphtheria, Pertussis, Measles, Mumps and Rubella at Birth among Healthy Term Indian Neonates
Authors: Verma Sanjay , James Deepak , Lavanya Jula , Rawat Amit , Venkataseshan Sundaram , Aggarwal Neelam
Published: December 2022

Background

The resurgence of vaccine preventable diseases in young infants is a matter of concern worldwide. Cord blood antibodies seroprevalence against various vaccine preventable diseases could reflect protection rates among adults, which could be important in providing protection in early infancy of newborn baby. Tdap vaccination is not yet part of immunization program for pregnant women in India.

Methods

Apparently healthy term newborns, delivered at a tertiary care hospital in Northern India, over two-year period were enrolled after taking informed written consent from their parents, and their cord blood sample was collected at birth. Ethical clearance was obtained from Institute Ethics Committee before starting enrollment.

Results

A total of 160 newborns (M:F=86:74) were enrolled. In our study, antibodies (IgG) against diphtheria toxin (DT) were >0.1 IU/ml in 44.4% (71/160), 0.01 to 0.1 IU/ml in 53.1% (85/160) and < 0.01 IU/ml in 2.5% (4/160). Only 44.4% of them were fully protected at birth against diphtheria.

Antibodies (IgG) against pertussis toxin (PT) >40 U/ml were seen in 41.2% (66/160). Out of these 66 children, 23 had titers >100 U/ml. Total of 58.8% (94/160) children had antibodies < 40 U/ml. Out of these 94 children, 48 had titers < 20 U/ml. Since correlates of protection in pertussis are not defined; those having titers >100 U/ml i.e. 14.3% were most protected; while those having titers < 20 U/ml were least protected.

Antibodies (IgG) against measles antigen were >12 IU/ml in 88.8% (142/160). Antibodies (IgG) against mumps antigen were >12 IU/ml in 83.1% (133/160). Antibodies (IgG) against rubella antigen were >12 IU/ml in 83.7% (134/160).

Conclusion

Protective antibodies against diphtheria and pertussis toxins were less in the studied newborns at birth making them susceptible to these diseases in early infancy, before primary vaccination commences. Tdap vaccination for pregnant mothers in India could help in improving these titers and protection in early infancy. Protective antibodies against measles, mumps and rubella in studied newborns at birth were satisfactory. For further enhancing protection, especially against rubella, one dose of MMR vaccine may be advised for women in child bearing age.

Acknowledgement: PGI Intramural Research Grant

Disclosures

All Authors: No reported disclosures.