bluuebunny/crossref_metadata_2025_split huggingface dataset:
657. Genomic Insights into Virulence Factors Affecting a Tissue-invasive Klebsiella pneumoniae Infection
Authors: Matono Takashi , Morita Masatomo , Nakao Nodoka , Teshima Yuji , Yamate Ryosuke , Hijikata Takamichi , Hoashi Kosuke , Ohashi Yusuke , Hasegawa Yuichi , Okinaka Tomohide , Ohnishi Makoto 
Published: December 2021

Abstract

Background
Japan is one of the hypervirulent Klebsiella pneumoniae (hvKp) endemic areas, resulting in an alarming issue in actual clinical settings. However, little is known regarding key virulence factors responsible for hvKp infection.

Methods
We analyzed K. pneumoniae isolates collected between 2017 and 2019, and defined hvKp as a pyogenic infection. Classical K. pneumoniae (cKp) involved a non-invasive infection or uncomplicated bacteremia. Isolates belonging to the K. pneumoniae species complex were excluded.

Results
We analyzed 112 isolates, including 19 hvKp, 67 cKp, and 26 colonizers, by whole-genome sequencing. Population genomics revealed that the K1-sequence type (ST) 82 clade was distinct from that of K1-ST23 clone (Figure 1). The virulence-gene profiles also differed between K1-ST82 (aerobactin and rmpA) and K1-ST23 (aerobactin, yersiniabactin, salmochelin, colibactin, and rmpA/rmpA2). The K2 genotype was more diverse than that of K1. A neighboring subclade of K1-ST23 (comprising ST29, ST412, ST36, and ST268) showed multidrug-resistance and hypervirulence potentials. Logistic-regression analysis revealed that diabetes mellitus was associated with K. pneumoniae infection (odds ratio [OR]: 4.11; 95% confidence interval [CI]: 1.14–14.8). No significant association was found between hvKp diagnosis and clinical characteristics, such as diabetes mellitus or community acquisition (Table 1). The K1 genotype (OR: 9.02; 95% CI: 2.49–32.7; positive-likelihood ratio [LR]: 4.08), rmpA (OR: 8.26; 95% CI: 1.77–38.5; positive LR: 5.83), and aerobactin (OR: 4.59; 95% CI: 1.22–17.2; positive LR: 3.49) were substantial diagnostic predictors of hvKp (Table 2).
Figure 1. Phylogenetic distribution of genetic virulence factors in 112 K. pneumoniae isolates

The highlighted strains are clinically pathogenic (orange, hypervirulent K. pneumoniae; yellow, classical K. pneumoniae; sky blue, colonization). The non-highlighted strain (NTUH-K2044) is a reference K. pneumoniae strain.

Conclusion
In hvKp-rich settings, diabetes mellitus, community-acquisition, and siderophores other than aerobactin were not remarkable predictors of hvKp infection. However, the K1 genotype, rmpA, and aerobactin were found to be substantial predictors, warranting clinical assessment of any possible/further pyogenic (metastatic) infection. We believe that these findings shed light on key hvKp virulence factors.

Disclosures
All Authors: No reported disclosures
661. Clinical Utility and Impact of the Metagenomic Microbial Plasma Cell-Free DNA Next-Generation Sequencing Assay on Treatment Decision: a Single-Center Retrospective Study
Authors: Noe Myint M , Shishido Akira A , Saharia Kapil , Luethy Paul 
Published: December 2021

Abstract

Background
Metagenomic next-generation sequencing (mNGS) of microbial cell-free DNA (mcfDNA) allows for non-invasive broad-range pathogen detection from plasma. The Karius® test that emerged in 2016 made mNGS widely available. However, there is little data describing the optimal role for this assay in clinical decision making.

Methods
We performed a single-center retrospective cohort study of adult patients for whom a Karius test was sent between May 2019 and February 2021 to assess clinical utility. We predefined criteria for clinical impact categories (Table 1) and stratified data by patient comorbidities, infectious syndromes, duration of antimicrobial therapy prior to Karius testing, reasons for sending the test, and final clinical diagnoses. Clinical impact was arbitrated by all authors after review and discussion of each case.

Results
A total of 80 patients were included. 45 patients (56%) were immunocompromised, and 14 (18%) had prosthetic hardware or grafts. The most common clinical syndrome was pneumonia/respiratory failure (31%), followed by sepsis/septic shock (15%) and endocarditis (13%). 72 patients (90%) received antibiotics prior to sending the Karius assay. The most common reason for sending the assay was unknown microbiologic diagnosis (78%), followed by avoiding invasive procedures (14%). The test was consistent with the final diagnosis in 65% of cases and had a positive impact in 34 (43%), a negative impact in 2 (3%), and uncertain or no impact in 44 (55%) (Table 2). A positive impact was observed in solid organ transplant recipients (SOTR, 71.4%, p=0.003), sepsis (71.4%, p=0.003), and those receiving antimicrobial agents for less than 7 days prior to Karius testing (i.e., 61.8%, p=0.004) (Table 3).

Conclusion
In our cohort, clinical utility of Karius testing was highest in SOTR and in patients with sepsis. Prolonged antimicrobial use ( &gt; 7 days) prior to Karius testing limited the utility of the assay. Prospective studies evaluating the utility of mNGS mcfDNA assays should be performed to further clarify its role in clinical management.

Disclosures
All Authors: No reported disclosures
662. Using Machine Learning to Aid in the Diagnosis of Multisystem Inflammatory Syndrome in Children
Authors: Soneji Maulin , Tan John , Wong Emily 
Published: December 2021

Abstract

Background
Multisystem inflammatory syndrome in children (MIS-C) is a newly recognized inflammatory syndrome that occurs post Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) infection. It affects multiple organ systems - particularly cardiac, gastrointestinal, dermatologic and neurologic. Clinicians may have difficulty diagnosing MIS-C due to its novelty and similarity to Kawasaki disease. Our goal was to use machine learning to predict whether children would have MIS-C based on symptoms and laboratory values.

Methods
A retrospective review was conducted of patients admitted to Loma Linda University Children’s Hospital who were suspected of having MIS-C. Demographic, symptom (such as fever, abdominal pain, diarrhea, shock, etc), and laboratory data were collected from the electronic medical record. For the 115 patients and 20 laboratory values, there was a total of 130 missing values (5.7%). Missing laboratory values were imputed using the median value based on the presence or absence of MIS-C. The data were split into a training (93 patients, 80%) and testing (22 patients, 20%) set. The training set was used to train a random forest model and the testing set was used to evaluate model performance. R 4.0.2 was used for modeling with the following packages: tidymodels and randomForest.

Results
There were 115 patients of which 49 were females, and 77 were diagnosed with MIS-C. The median age of the patients with MIS-C was 115 months and 79 months for those without MIS-C. In the testing set, all 15 patients with MIS-C were classified correctly but of the 7 without MIS-C, the model predicted 4 of the patients correctly. This gives a sensitivity of 100% and specificity of 57%. When changing the seed and testing set, the sensitivity remained 100% but the specificity improved to 86%. The random forest algorithm showed that the most important features were pro-calcitonin, ferritin, pro-BNP, and CRP.

Conclusion
During the height of the SARS-CoV-2 pandemic, many children were being admitted with suspected MIS-C, but clinicians struggled to confirm the diagnosis. We have found a model predicting which of these patients had MIS-C with high sensitivity. This model is a first step of many toward creating the foundation of personalized medicine for children.

Disclosures
All Authors: No reported disclosures
664. Clinical Impact of Cell-Free DNA Metagenomics in Diagnosing Infectious Diseases in Pediatrics: A Single-Center Experience
Authors: Otto William , Dumm Rebekah , Fatemi Yasaman , Swami Sanjeev K 
Published: December 2021

Abstract

Background
Metagenomic next-generation sequencing (mNGS) of plasma cell-free DNA has significant potential to improve infectious diseases diagnostics through unbiased detection of pathogens. However, the optimal patient population or clinical condition for this testing has not been determined.

Methods
We performed a retrospective review of all orders for plasma cell-free DNA mNGS using the Karius test (Karius, Redwood City, CA) from The Children’s Hospital of Philadelphia from 7/1/19-4/30/21. Chart review then determined if the test had a positive, negative, or no clinical impact.

Results
25 mNGS tests were ordered on 24 unique patients. The majority of tests were ordered on immunocompromised patients (Table 1). Most mNGS tests were ordered after completion of routine microbiological testing (17/25, 71%). Three tests were not completed as ordered. Most completed tests (18/22, 82%) had no impact on clinical care as they confirmed the known diagnosis or were not acted upon (Figure 1). mNGS testing had a positive impact in 2 cases. For one patient with congenital heart disease presented with persistent fever and concern for endocarditis despite negative infectious workup, a negative mNGS result allowed for continued monitoring without therapy. Another patient with a lymphatics disorder had mNGS performed due to persistent clinical instability; testing was positive for Candida parapsilosis, allowing for early initiation of antifungal therapy. However, test results had a negative clinical impact in 2 other patients. In a patient with congenital heart disease and fever, identification of two organisms led to prolonged antibiotic therapy for endocarditis without resolution of symptoms. In a patient with leukemia, report of a dematiaceous mold led to further diagnostic testing, including a lumbar puncture, as well as treatment with antifungal therapy despite no clear diagnosis.

Table 1

Conclusion
In this study, the majority of plasma cell-free mNGS tests had no impact on clinical care. mNGS testing did positively impact care in 2 patients, but did had a negative impact on care in 2 instances, leading to further testing and unnecessary treatment. Further investigation is needed to determine the ideal population or clinical condition for testing and the ideal time of sending plasma cell-free mNGS tests.

Disclosures
All Authors: No reported disclosures
665. Clinical and Financial Impact of Next Generation Sequencing (NGS) in addition to Conventional Microbiology Testing in our Urban Referral Health Center
Authors: Saini Vikram , Jaber Tariq , Como James D , Abdulmassih Rasha , Min Zaw , Bhanot Nitin 
Published: December 2021

Abstract

Background
Clinical microbiology traditionally relies on culture methodology and serological testing, that have inherent limitations. Newer diagnostic techniques such as Next Generation Sequencing (NGS) have shown promise to improve microbial identification. In select scenarios, we send clinical specimens to reference laboratories for NGS testing in addition to current standard of care (SOC) diagnostics. We wanted to determine how this diagnostic approach has impacted patient care. We also wanted to review the financial burden through cost-benefit analysis for these ‘send-out’ tests.

Methods
We performed a retrospective chart review of all cases over a 3-year period in which NGS was submitted. Data, including demographics, comorbidities, antimicrobial use, and diagnosis (by SOC and NGS) were gathered. We delineated how often there was concordance or discordance between SOC and NGS. We also obtained information on financial cost (direct and indirect) and turnaround time (TAT) for NGS results.

Results
A total of 33 clinical specimens from 25 patients were sent for NGS. The majority of specimens comprised joint tissue/fluid, organ tissue and CSF.
Concordance occurred between SOC and NGS testing in 75.8% (25/33) of samples; of those, 88% excluded infection. NGS identified a pathogen in 20% (5/25) patients in which concomitant SOC testing was negative. A subsequent change in antimicrobial management occurred in 16% (4/25) of patients. The mean TAT was 14 days and average cost per specimen was &821.52 (range: &573-&1590).
Table 1. Pathogens identified by NGS with negative traditional microbiological test results

Figure 1. Distribution of specimen site (in %) sent for NGS

Conclusion
NGS can provide additional diagnostic sensitivity in infectious diseases, which at our institution identified a new pathogen in 20% and a resultant treatment change in 16% of our patients. This testing may also allow physicians to reaffirm the absence of an infection diagnosis. A larger NGS testing population may reveal more significant benefits. While the attributable cost of NGS was substantial, it should be measured against the costs of administration of unnecessary antibiotics, inaccurate diagnosis, and adverse patient outcomes that may result from SOC testing alone. Considering its financial cost and extended TAT, in-house NGS testing may be warranted to facilitate a higher volume of testing.

Disclosures
All Authors: No reported disclosures
667. Next Generation Sequencing of Microbial Cell Free DNA in the Diagnosis and Treatment of Infectious Disease in Children: When Does the Result Justify the Cost?
Authors: Quick Rachel Downey , Martinez Kelli A , Russo Susan M , McGwier Sarah E , Quirt Rachel A , Hauger Sarmistha Bhaduri , Fernandez Mariosl , Murphey Donald 
Published: December 2021

Abstract

Background
Pathogen testing using next-generation sequencing of microbial cell-free DNA (NGS cfDNA) is a promising diagnostic tool to identify pathogens that might not be detected using conventional lab evaluation. Considering the cost of this test, it is important to determine when it is most useful to the plan of care (POC).
Figure 1. Unit of admission among cases

Figure 2. Patient characteristics in cases determined to be valuable and not valuable to the plan of care (POC)

Methods
In this retrospective study, we collected data from the medical charts of 50 consecutive NGS cfDNA tests in a free-standing children’s hospital. We evaluated patients for demographics, underlying conditions, diagnosis at time of testing, conventional laboratory testing and timing, medical treatment, and NGS cfDNA test results for clinical relevance or false negative results compared to conventional testing. The primary goal was to identify patients for whom the NGS cfDNA testing affected the POC. Charts were reviewed, and determinations regarding whether the result influenced the POC were confirmed by a provider.

Results
We were unable to differentiate patients with clinically valuable NGS cfDNA results (Fig 1 & 2). Among those with NGS cfDNA results valuable to the POC (n=22), both negative and positive testing guided POC (13 valuable negative vs. 9 diagnostic cases). In the total sample, 5 cases (10%) had a clinically relevant pathogen identified through conventional testing, but not through NGS cfDNA and 2 cases had antimicrobial resistance on culture, which is not detected by NGS cfDNA.

Conclusion
While we did not find a specific clinical profile for NGS cfDNA use, positive results were essential to the diagnosis in 18% of cases with otherwise negative laboratory evaluation for the pathogen identified in NGS cfDNA. Negative tests affected the POC in 26% of cases by avoiding unnecessary antimicrobials in high risk immunocompromised patients and patients that presented with low-risk of infection, but unclear disease process.
Caution must be exercised with reliance on this test with respect to antimicrobial resistance and risk of false negative results.

Disclosures
All Authors: No reported disclosures
668. Restricting Ordering of Multiplex Gastrointestinal Panel Improves Test Utilization
Authors: Tai Don Bambino Geno , Misra Anisha , Sampathkumar Priya , O'Horo John C 
Published: December 2021

Abstract

Background
The multiplex gastrointestinal pathogen panel (GIP) is a convenient and quick diagnostic test for determining the infectious etiology of diarrhea. It identifies several of the most common pathogens associated with gastroenteritis. However, it is expensive, and test results may not impact care, given that several of the pathogens in the panel are managed expectantly. We describe our experience with a diagnostic stewardship initiative to resolve the overuse of this testing method.

Methods
We performed a pre/post study of GIPs ordered for inpatients 18 years old and older from December 19, 2018, to December 18, 2020, at Mayo Clinic hospital in Rochester, Minnesota. GIP orders for inpatients were limited to the first 72 hours of hospitalization starting December 19, 2019. Orders after 72 hours were encouraged to be changed to Clostridioides difficile NAAT testing or sent to an infectious disease provider to override on a case-by-case basis. Our hospitals used BioFire® FilmArray® Gastrointestinal Panel (BioFire Diagnostics, Salt Lake City, Utah).

Results
A total of 2,641 GIPs were performed during the study period. There were 1,568 GIPs (3.3/100 hospitalizations) in the pre-intervention period compared to 1,073 (2.6/100 hospitalizations) post-intervention, representing a drop of 21.2%. The most common pathogen detected was C. difficile (toxin A/B) (48.8%, n=402), followed by norovirus (17.5%, n=144). The overall test positivity rate was 27.9% (n=736). The test positivity rate decreased 1.8% from 28.6% (n=448) to 26.8% (n=288) after the restriction (p=0.33). The proportion of C. difficile among all pathogens detected increased from 48.5% to 49.7% (p=0.67).
Table 1. Pre- and Post-Intervention Test Positivity Rate of Specific Pathogens in GIP

Conclusion
Our study showed that restricting the ordering of GIP to the first 72 hours of hospitalization and directing providers to standalone C. difficile NAAT testing resulted in a reduction of GIPs performed. There were marginal changes in the test positivity rate of GIP. A limitation of our study is that the timing of post-intervention coincided with the COVID-19 pandemic, which had unpredictable effects on hospital practice and patient admissions. Ideally, future quality improvement projects should increase the test positivity of pathogens other than C. difficile while lowering the GIP use in diagnosing C. difficile colitis.

Disclosures
John C. O'Horo, Sr., MD, MPH, Bates College and Elsevier Inc (Consultant)
670. Precision Metagenomic (PM) Sequencing Outperforms Conventional Urine Culture in Detecting Clinically Relevant Microorganisms
Authors: Stinnett Rita C , Kent Bethany , Mangifesta Marta , Kadam Anagha , Xie Heng , Stauffer Stacie , Lemon Jamie , Briggs Benjamin , Farnaes Lauge , Schlaberg Robert 
Published: December 2021

Abstract

Background
Morbidity from urinary tract infection (UTI) is high. Urine culture is the reference method for UTI diagnosis. Its diagnostic yield is limited as prior antibiotic use prevents growth of established uropathogens, many emerging uropathogens do not grow under routine culture conditions, and results interpretation can be subjective. Faster, more comprehensive diagnostics could help manage recurrent and/or drug-resistant infections. We evaluated the diagnostic yield of a precision metagenomic (PM) workflow for pathogen detection & antimicrobial resistance (AMR) characterization directly from urine.

Methods
Residual urine samples from symptomatic adults evaluated by culture & susceptibility were identified by a combination of consecutive & stratified random sampling (n=480; 79% culture positive). DNA was extracted with modifications to the Quick-DNA Urine Kit (Zymo). Libraries were generated with Illumina DNA Prep with Enrichment for clinically relevant targets (191 pathogens, 1976 AMR markers) with the Explify Urinary ID/AMR Panel (UPIP, IDbyDNA). Enriched libraries were sequenced on the NextSeq550 (Illumina) and data analyzed with the Explify UPIP Data Analysis Solution (IDbyDNA).

Results
For bacterial uropathogens, 94% positive agreement was observed between this PM workflow and culture. PM detected fastidious and/or anaerobic potential uropathogens in 30% and 7% of samples reported as culture-negative or positive for other bacteria, respectively. Total agreement between AMR marker detection and phenotypic resistance was 78%. Notably, PM predicted phenotypes of ESBL E. coli and K. pneumoniae (10/10), MRSA (9/9), and vancomycin-resistant E. faecium (4/5). PM also detected pathogens associated with sexually-transmitted infection (C. trachomatis, HSV) and bacterial vaginosis (G. vaginalis). PM produced complete results within 24-36 hours of sample receipt (vs culture & susceptibility: 42-72 hrs).

Conclusion
The sensitivity of PM for uropathogen detection was noninferior to culture (Δ = 0.05; Nam RMLE; p &lt; 0.0005). PM predicted antimicrobial resistance phenotypes for common uropathogens and identified potential pathogens not detected by conventional culture. Future studies should assess the impact of PM-guided management on clinical outcomes.

Disclosures
Rita C. Stinnett, PhD, MHS, IDbyDNA (Employee) Marta Mangifesta, PhD, IDbyDNA (Employee) Anagha Kadam, PhD, IDbyDNA (Employee) Heng Xie, PhD, IDbyDNA (Employee) Stacie Stauffer, BS, IDbyDNA (Employee) Jamie Lemon, PhD, D(ABMM), IDbyDNA (Employee) Benjamin Briggs, MD, PhD, IDbyDNA (Employee) Lauge Farnaes, MD, PhD, Cardea Bio (Advisor or Review Panel member)IDbyDNA (Employee) Robert Schlaberg, MD, MPH, IDbyDNA (Consultant, Shareholder, Co-founder)
674. Evaluation of the Access Bio CareStart™ Rapid SARS-CoV-2 Antigen Test in Asymptomatic Individuals Tested at a Community Mass-testing Program in Western Massachusetts
Authors: Matias Wilfredo , suliman Sara , Fulcher Isabel , Molano Francisco , Collins Shannon , Uceta Elizabeth , Zhu Jack , Paxton Ryan , Gonsalves Sean , Harden Maegan , Fisher Marissa , Meldrim Jim , Gabriel Stacey , Franke Molly , Hung Deborah , Smole Sandra , Madoff Lawrence , Ivers Louise 
Published: December 2021

Abstract

Background
Point-of-care antigen-detecting rapid diagnostic tests (RDTs) to detect Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) represent a scalable tool for surveillance of active SARS-CoV-2 infections in the population. Data on the performance of these tests in real-world community settings will be paramount for their implementation to combat the COVID-19 pandemic.

Methods
We evaluated the performance characteristics of the CareStartTM COVID-19 Antigen Test (CareStart) in a community testing site in Holyoke, Massachusetts. We compared CareStart to a SARS-CoV-2 reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) reference, both using anterior nasal swab samples. We calculated the sensitivity, specificity, and the expected positive and negative predictive values at different SARS-CoV-2 prevalence estimates.

Results
We performed 666 total tests on 591 unique individuals. 573 (86%) were asymptomatic. There were 52 positive tests by RT-qPCR. The sensitivity of CareStart was 49.0% (95% Confidence Interval (CI): 34.8 – 63.4) and specificity was 99.5% (95% CI: 98.5 – 99.9). Among positive RT-qPCR tests, the median cycle threshold (Ct) was significantly lower in samples that tested positive on CareStart. Using a Ct less than or equal to 30 as a benchmark for positivity increased the sensitivity of the test to 64.9% (95% CI: 47.5 – 79.8).

Performance characteristics of CareStart test results benchmarked against the RT-qPCR gold standard (excluding undetermined results).

Examples of images of CareStart rapid test showing variable band intensities.

N2 gene RT-qPCR Cycle threshold (Ct) values corresponding to positive and negative CareStart rapid antigen test results for all RT-qPCR positive samples (n=52).

Conclusion
Our study shows that CareStart has a high specificity and moderate sensitivity. The utility of RDTs, such as CareStart, in mass implementation should prioritize use cases in which a higher specificity is more important, such as triage tests to rule-in active infections in community surveillance programs.

Disclosures
All Authors: No reported disclosures