bluuebunny/crossref_metadata_2025_split huggingface dataset:
555. Clinical impact and real-life utilization of Karius testing: a retrospective analysis of cases from an urban, academic medical center
Authors: Conway-Pearson Liam , Orner Erika , Thwe Phyu , Szymczak Wendy , McCort Margaret E 
Published: November 2023

Abstract

Background
Metagenomic next-generation sequencing (NGS) of microbial cell-free DNA is a relatively novel diagnostic technique that may potentially expedite and/or supplement pathogen-specific infectious disease diagnoses, minimize the time to appropriate antibiotic therapy, and reduce unnecessary and invasive testing. However, careful diagnostic stewardship is necessary to ensure that such tests are being ordered in the appropriate patient population.

Methods
A retrospective chart review of all patients for whom the Karius NGS test was sent at our institution between Jun 13, 2020-Jul 22, 2022 was performed. Clinically relevant pathogens were defined as diagnoses that led to change in antimicrobial therapy. Stata statistical software (version 17.0, College Station TX) was used to analyze patient and hospitalization risk factors associated with Karius testing.

Results
Thirty cases among 29 unique patients for whom Karius testing was performed were included in our review. Patient characteristics are shown in Table 1. Twenty-one patients (72%) were immunocompromised, including 14 (47%) with solid organ transplant (SOT) and 9 (30%) with malignancy. Mean hospital length of stay (LOS) prior to Karius test collection was 15.8 days (+/- 21.6 days, range 1-120). Reasons for sending Karius are shown in Fig 1. Three patients (10%) had tissue-specific NGS testing performed in addition to Karius. On average, patients received 13.9 days of antibiotics prior to Karius (+/-10.11, range 0-37). Mean turnaround time for Karius results was 38.3 hours (+/- 16.5, range 23-79). Ten (34.5%) Karius results identified no pathogens. Karius identified fungal organisms in 3 (10%) tests, one of which correlated with true infection. Karius results correlated with other infectious diagnostics (such as viral PCR or cultures) in 10 (33%) cases. Clinically relevant pathogens (not identified by other testing) were identified by Karius in only 3 (10%) cases. There was no statistically significant correlation between pathogen detection by Karius and history of HIV (p=0.27), transplant (p=0.70), malignancy (p= 0.21), or number of days from admission to test (p=0.66)
Table 1
Patient characteristics (N=29 unique patients, 30 tests)
Figure 1
Reasons for Karius test

Conclusion
Metagenomic NGS is an exciting area of diagnostic innovation, but more studies are needed to determine when and where this test is best utilized.

Disclosures
All Authors: No reported disclosures
556. Commercial Microbial Cell-Free DNA Next-Generation Sequencing in a Pediatric Quaternary Care Facility Yields Limited Diagnostic Utility
Authors: Osborn Lucas J , Kamel Dina , Malhotra Sanchi , Posch Leila C , Costales Cristina , Bard Jennifer Dien 
Published: November 2023

Abstract

Background
Microbial cell-free DNA next-generation sequencing (mcfNGS) is a novel diagnostic tool increasingly utilized as a rapid, noninvasive approach to aid in the diagnosis of infectious diseases. However, its utility in pediatric patients is not well established. This study aimed to explore the diagnostic utility of commercial microbial cell-free DNA sequencing in a pediatric quaternary care facility.

Methods
This retrospective study included 15 patients with mcfNGS results between June 2018 and April 2023. Chart abstraction was performed to determine changes in clinical management. Change in management was defined as any clinical decision implemented based on mcfNGS results. Overall clinical impact was defined as either a beneficial or deleterious change in patient outcome resulting from clinical management changes made based on mcfNGS results.

Results
Of the 15 patients, a total of 14 valid results were reported, 13 (86.7%) of which were from the first attempt. At least one microbial target was detected in 10/14 (71.4%) patients. Standard microbiology testing (SMT) revealed a pathogen or diagnostic marker of such in 8/14 (57.1%) patients. Notably, there were no instances in which mcfNGS detected a true pathogen in the context of negative SMT. Of the 14 patients with valid reports, clinical management was changed based on mcfNGS in 3 (21.4%) patients. This included addition of anti-fungal therapy, de-escalation of antimicrobials, and initiation of immunosuppressive corticosteroid therapy in the context of a negative mcfNGS result. Of the 10 patients in which at least one microorganism was detected, 70% were determined to be either contamination or of unclear clinical significance. There was only one instance in which mcfNGS alone led to a beneficial clinical impact as determined by de-escalation of anti-fungal therapy.
Figure 1.
mcfNGS was performed on 15 pediatric patients between July 2018 and April 2023. Pie chart represents categorization of mcfNGS results and their clinical impact.

Conclusion
While infectious disease metagenomic NGS holds great promise, the utility of currently available commercial assays for non-invasive specimens remains poorly understood. Here we report that in a small cohort of pediatric patients, commercial mcfNGS added minimal value over standard microbiological testing. Additional investigation is required to determine the ideal clinical picture warranting mcfNGS.

Disclosures
Jennifer Dien Bard, PhD, Abbott Molecular: Grant/Research Support|BioMerieux: Advisor/Consultant|BioMerieux: Grant/Research Support|BioMerieux: Honoraria|Genetic Signature: Advisor/Consultant|Genetic Signature: Grant/Research Support|Luminex: Grant/Research Support|Salve: Stocks/Bonds|Thermo Fisher: Honoraria
557. Cost-effectiveness of Introducing Metagenomic Next-generation Sequencing (mNGS) for the Diagnosis of Suspected Neurological Infections Patients in China
Authors: Peng Siyang , Liang Rui , Liu Peng , Hu Long , Ai Yaping , Wang Junfeng , Hong Guanqi , Qu Shuli 
Published: November 2023

Abstract

Background
Early identification of neurological pathogens is crucial for favorable clinical outcomes. Metagenomic next-generation sequencing (mNGS) offers an alternative approach to identify pathogens in complex clinical samples. This study aimed to assess the cost-effectiveness of using mNGS in combination with traditional methods in diagnosing suspected neurological infections patients.

Methods
A decision tree model was developed to illustrate the clinical pathway for patients with suspected neurological infections in China. Two strategies were compared, one utilizing mNGS combined with traditional pathogen detection methods, and the other relying solely on traditional methods including cerebrospinal fluid microbial culture, smear microscopy, and serological tests. The study was conducted from the Chinese healthcare system perspective. Survival outcome, life years outcome and cost outcomes were captured over a lifetime horizon. Model inputs, including cost (specimen collection cost, diagnosis cost, imaging examination cost, drug cost and inpatient bed cost), treatment efficacy, mortality, sensitivity and specificity of different testing strategies, were derived from published literature and experts’ interviews. Uncertainty was assessed by sensitivity analyses.

Results
The base case analysis suggested that, compared with traditional pathogen detection methods, mNGS combined with traditional methods resulted in longer life-year (average 0.04 life-year gain) and lower cost (average saving of 6,419 CNY (947 USD)), among all patients tested. The life-years gain was primarily driven by the more accurate diagnosis and the consequent administration of more effective etiological treatment. The cost saving was largely driven by the reduction of drug costs which resulted from precision medicine-based treatment, instead of empirical treatment. The probabilistic sensitivity analysis confirmed the robustness of the model.

Conclusion
Compared to traditional methods only, mNGS combined with traditional methods is a cost-effectiveness method for improving patient clinical outcomes while reducing healthcare costs.

Disclosures
All Authors: No reported disclosures
561. Microbial Analysis and Fungi-Bacteria Correlation in Chronic Wound Infection Patients
Authors: Wang Qingqing , Hu Bijie 
Published: November 2023

Abstract

Background
Chronic wound infection has become a major healthcare burden globally. The colonized microbiome features and correlation between bacteria and fungi have not been listed.

Methods
In this study, we enrolled 38 acute wound infection and 28 chronic wound infection patients. The wound swabs sampling at admission were tested by metagenomic next-generation sequencing. Microbial community characteristics in wound infection patients and bacteria-fungi correlations in chronic wound infection patients were analyse after filtering background organisms.Figure 1.Flow chart

Results
We found that wound microbiome in chronic wound infection patients had higher abundance of Pseudomonas aeruginosa than that in acute wound patients. Meanwhile, microbes with high relative abundant in chronic infection wounds were less significantly association with plasma inflammation factors compared with those in acute infection wounds. Finally, we investigated the association between fungi and bacteria in chronic infection patients and found that relative abundance of Pseudomonas aeruginosa was negatively associated with that of Candida albicans.Figure 2.Comparison of bacteria species relative abundance between groups.Barplot of average relative frequencies of genera. Only genera&gt;1% of relative abundance in wound were represented. C= chronic infection wound group, NC= acute infection wound groupFigure 3.Analysis of Linear Discriminant Analysis (LDA) Effect Size in groups.The bar graph showed pathogens with LDA score log10 &gt;5 in two groups. C= chronic infection wound group, NC= acute infection wound group.Figure 4.Fungi-bacteria network in patients with chronic infection wound.Green dots: bacteria; Blue dots: fungi; red edge: positive correlation; green edge: negative correlation. Relative abundance of Pseudomonas aeruginosa was negatively associated with that of Candida albicans highlighted with red box.

Conclusion
Our metagenomic sequencing results of wound supported that Pseudomonas aeruginosa may be the biomarker of chronic wound infection and have interaction with candida albicans.

Disclosures
All Authors: No reported disclosures
562. Diagnostic accuracy comparison of the Biofire Filmarray pneumonia panel versus routine diagnostic methods for diagnosis of ventilator associated pneumonia: a real life study
Authors: García-Martínez Alejandra , Rojo-Gutiérrez Leticia , Llanes-Somellera Sergio , Aguilar-Zapata Daniel 
Published: November 2023

Abstract

Background
In Mexico, the Hospital Epidemiological Surveillance Network previously the COVID-19 pandemic, reported a total of 61,969 health care associated infections with an incidence rate of 4.7 per 100 discharges, 20.7% of which were categorized as ventilator associated pneumonia.
Biofire Filmarray pneumonia panel has been accepted as a tool for early and rapid diagnostic of pneumonia with recognition of several hospital acquired pathogens including resistant genes. However, there are some mismatch in the multiplex PCR detection and the culture isolation.

Methods
An observational, comparative, retrospective, non-randomized, cross-sectional, open study was performed using files from patients diagnosed with ventilator associated pneumonia who underwent diagnostic testing on culture and PCR multiplex FilmArray pneumonia panel to determine diagnostic accuracy.
Intensive care unit files from August 2021 to February 2022 with ventilator associated pneumonia with airway samples for Filmarray pneumonia panel and cultures. Evaluation of the used diagnostic tests was carried out using: sensitivity, specificity, positive predictive value and negative predictive value.

Results
55 patients were included, each of them with both test. 72% of the study population were males, with a mean age of 61 years. 76% of the population had severe COVID-19.
E.Coli had 100% sentitivity and 96% specificity , P. aeruginosa 100% sentitivity and 88% specificity, E.Cloacae 100% sentitivity and 91% specificity, and S. aureus had 100% sentitivity and 89% specificity on Biofire Filmarray pneumonia panel. While K. pneumoniae had 50% sensitivity and 89% specificity. NPV was 98% for K. pneumoniae, and 100% for E. coli, P. aeruginosa, E. cloacae, and S. aureus.
S.maltophilia was isolated in 3 culture samples and the Filmarray pneumonia panel was reported negative because lacking of testing this microorganism, as well as 1 A. fumigatus isolation.
Samples for cultures and Biofire FilmArray pneumonia panel
The different samples that were included from 55 patients in this study correlated with pneumonia panel and conventional cultures.
PCR Biofire FilmArray pneumonia panel diagnostic study evaluation
Each of the microorganism that had correlation between Filmarray pneumonia panel compared with conventional cultures

Conclusion
Biofire Filmarray pneumonia panel provides early and accurate information on pathogens causing ventilator associated pneumonia. However it cannot replace conventional culture because of lacking of some microorganism detection. It provides a useful tool for early decision-making in treatment.

Disclosures
All Authors: No reported disclosures
563. Mycoplasma genitalium with Fluoroquinolone Resistance: Design and Development of a Multiplex Real-Time PCR Assay for Detection and Differentiation
Authors: Alabyev Boris , Ankoudinova Irina , Scarr Noah , Decker Becca , Lukhtanov Eugene 
Published: November 2023

Abstract

Background
Mycoplasma genitalium is a sexually transmitted bacterium causing urethritis in men and associated with cervicitis and pelvic inflammatory disease in women. Only a few antimicrobial classes have activity against mycoplasmas. The first-line treatment for M. genitalium infections is doxycycline followed by azithromycin. Due to overuse of azithromycin to treat infections, resistance to azithromycin has been rapidly increasing. The moxifloxacin of fluoroquinolones family of antibiotics was 100% effective against M. genitalium, but recently the resistance markers for fluoroquinolone treatment have also emerged. Multiple studies attribute fluoroquinolone treatment failure to single nucleotide polymorphisms (SNPs) in parC and gyrA genes.
We aim to demonstrate proof of principle for a Real-Time PCR assay that simultaneously detects M. genitalium and fluoroquinolone resistance.

Methods
The MGB Alert M. genitalium with fluoroquinolone resistance RUO Detection Reagent is a multiplex of real-time PCR reagents that simultaneously detect M. genitalium DNA and distinguish fluoroquinolone resistance-associated mutations and wild type in M. genitalium. The assay targets parC and gyrA genes and includes a set of two primers and two probes specific to M. genitalium. The DSQ probe identifies the species DNA. The Pleiades hybridization probes serve to identify and distinguish a wild type genotype and several known resistance-conferring point mutations by melt curve analysis.

Results
Analytical Study:
Analytical sensitivity was determined and verified at 1.42 copy of bacterial genome per reaction.
A linear range was established from 1e7 to 10 genome copies per reaction.
Test results showed no cross-reactivity with organisms that might be present in normal vaginal swabs and urine specimens.

Conclusion
Preliminary analytical evaluation of the MGB Alert M. genitalium with fluoroquinolone resistance RUO Detection Reagent indicates potential as a valuable tool in the diagnosis of M. genitalium and resistance guided treatment.

Disclosures
Boris Alabyev, PhD, ELITechGroup MDx LLC: Salary Irina Ankoudinova, MS, ELITechGroup MDx LLC: Salary Noah Scarr, BS, ELITechGroup MDx LLC: Salary Becca Decker, BS, ELITechGroup MDx LLC: Salary Eugene Lukhtanov, PhD, ELITechGroup MDx LLC: Salary
564. Nocardiosis in Portugal: a single-center experience
Authors: Besteiro Bruno , Coutinho Daniel , Fragoso Joana , Figueiredo Cristovão , Nunes Sofia , Azevedo Carlos , Teixeira Tiago , Selaru Aurelia , Lameirão Angelina , Malheiro Luis 
Published: November 2023

Abstract

Background
Nocardiosis is a rare opportunistic infection with increasing incidence. Given its rarity, data on the prognosis and distribution are scarce and essential.

Methods
Retrospective study reviewing all nocardiosis cases diagnosed at our tertiary care hospital from January 2019 to January 2023.

Results
A positive Nocardia spp. culture was identified in 20 patients. Nocardia isolation was considered colonization in 2 patients, but the other 18 cases were considered as disease, 6 (33.3%) of which were classified as disseminated nocardiosis (DN). The mean
age was 64.0±14.05 years-old and 75% were males. One or more immunosuppressive conditions were identified in 70% of patients, including diabetes mellitus (n=9), active solid tumors (n=3), autoimmune diseases (n=3) and HIV infection with CD4+ &lt; 200 cel/uL (n=2). Among the immunocompromised patients, 28,6% were being treated with high-dose corticosteroid therapy. The lung was the most common site of infection (85%) and most cultures were initially retrieved for lower respiratory tract samples (85%) evaluated for mycobacteria in modified Middlebrook 7H9 Broth. Lymphopenia was observed in 38.9% of patients.The most frequently isolated species were N.nova/africana (n=7), N.cyriacigeorgica (n=4) and N.pseudobrasiliensis (n=3). N.cyriacigeorgica was identified in the two cases considered colonization. Most patients (94.4%) were treated with antimicrobials, 50.0% in monotherapy and 44.4% in combination therapy. The most frequently prescribed antibiotics were co-trimoxazole (94.4%), imipenem (22.2%) and linezolid (16.7%). Selected antimicrobial agents were generally effective, with linezolid and co-trimoxazole having the highest susceptibility rates (100% susceptibility). The median [IQR] duration of treatment was 238 [45–720] and 170 [5–360] days for localized and DN, respectively. The overall one- year case fatality was 25% and was higher in patients with DN (80%).

Conclusion
Nocardiosis is an uncommon but emerging disease which can occur both in immunocompetent and immunocompromised patients. The present study reports a case series on Nocardiosis from Portugal and provides important information of this disease. As the
outcomes are poor, early recognition and prompt treatment are essential to improve the outcome.

Disclosures
All Authors: No reported disclosures
567. Performance of IgM and IgG antibodies against Bartonella henselae for diagnosis of Cat Scratch Disease in pediatric patients
Authors: Caratozzolo Ana M , Toledano Analía , Praino María Laura , Ferolla Fausto Martín , Neyro Silvina , Cazes Claudia Inés , López Eduardo L 
Published: November 2023

Abstract

Background
Bartonella henselae infection causes Cat Scratch Disease (CSD). Lymphadenopathy is the most common symptom and a small percentage of patients have systemic impairment. CSD can mimic malignancy and manifest atypically, therefore reliable serological testing has clinical importance. CSD is diagnosed if two of the following criteria are met: 1) the presence of clinical symptoms consistent with CSD; 2) the existence of antibodies against B. henselae IgM and/or IgG (1:256) (Fig.1). We aim to assess the accuracy and diagnostic utility of IgM and IgG in pediatric patients with suspected CSD.Fig. 1:Immunofluorescence AssayPositive IgM against B. henselae

Methods
A retrospective, observational and analytical study was carried out from April 2022 through April 2023. Medical and laboratory records of patients with follow-up in the Infectious Diseases Department of a Children's Hospital in Buenos Aires (Argentina) were evaluated.

Results
We included 244 serum samples from patients with clinical suspicion of CSD using Immunofluorescent assay (IFA).
Median age: 84 (IQR 48-132) months, 137 were female, 95% (233/244) had cat interaction.
Twenty eight percent (70/244) were diagnosed with CSD based on serological evidence: 83,9% (58/70) had IgM +/IgG + (group 1); 10% (7/70), IgM-/IgG+ &gt;1/64 (group 2) and 7,15% (5/70), IgM+/IgG – (group 3). The average time of symptom onset was 22,8 (6-90) days for group 1, 29,4 (11-90) days for group 2, and 11,4 (5-15) days for group 3.
Lymphadenopathy was found in 87,1% (61/70) with or without systemic involvement and 6 % (4/70) had systemic involvement without lymphadenopathy.
IgM had Sensitivity: 89%, Specificity: 97%, Positive Predictive Value (PPV): 92% and Negative Predictive Value (NPV) : 96%.

Conclusion
Between 5-15 days after the onset of symptoms, IgM allowed us to diagnose 5 patients with CSD. The identification of IgM antibodies in CSD patients with systemic impairment has a great diagnostic performance. IgM remained positive after 90 days . We were able to diagnose CSD in 7 patients between 11 and 28 days following the onset of symptoms due to the presence of IgG 1:256 or higher. Combination of different methods (e.g., clinical and serological) and a correct time of sampling, greater than 5 days, should be considered for rapid and accurate CSD diagnosis.

Disclosures
All Authors: No reported disclosures