bluuebunny/crossref_metadata_2025_split huggingface dataset:
620. Development and Validation of a Novel qPCR Assay for Differentiation of Common Candida Pathogens including C. auris
Authors: Thomas Clayton , Grantham James , Lute Emily , Davidson Jerod , Cowden Scott , Nutt Jamie 
Published: November 2023

Abstract

Background
Candida is a common asymptomatic fungal colonizer of humans. Of the 200+ total species in the genus Candida, only a few are known to cause infection. The most common are C. albicans, C. glabrata, C. parapsilosis, C. tropicalis, C. krusei, and C. auris. In the USA, candidemia is the fourth most common cause of bloodstream infections in hospitalized patients. Although antifungal medication can treat candidemia, mortality rates remain between 30 and 60%. Eurofins Viracor has developed a qPCR assay that will qualitatively detect and differentiate any of the 6 previously listed Candida species in whole blood. Speciation is critical for treatment due to variable drug susceptibility among different species, particularly C. auris due to its multi-drug resistance.

Methods
Multiple primer/probe mixes were designed around and within the ITS1, 5.8s, ITS2, and 28s ribosomal subunit regions in each of the six Candida target species. The 5.8s and 28s regions are heavily conserved, while the ITS regions are highly divergent and used to differentiate species. After optimization, the six primer/probe mixes were partially multiplexed resulting in four mixes covering all species. DNA was extracted from human blood spiked with viable Candida using the MagMAX™ DNA Multi-Sample Ultra 2.0 Kit, and eluates were amplified using the Applied Biosystems™ 7500 Fast platform.

Results
Each assay met all validation acceptance criteria and demonstrated excellent accuracy, precision, linearity and dynamic range, and sensitivity. 32 non-Candida fungal and bacterial pathogens that commonly cause bloodstream infections were used to assess specificity. All specificity samples were negative for all Candida targets. To assess accuracy, 75 of 75 Candida samples representing all six species across a range of concentrations were tested and correctly identified. 24 of 25 known-negative samples were negative, with one positive C. glabrata CT result observed just below the cutoff.

Conclusion
Traditional blood culture methods for Candida species identification can be too time consuming for a quickly progressing infection. The Candida qPCR assay described here not only detects an infection faster but provides accurate speciation allowing for rapid and targeted antifungal treatment options for the patient.

Disclosures
Clayton Thomas, BS in Biology, Eurofins Viracor: Employee James Grantham, n/a, Eurofins Viracor: Employee Emily Lute, n/a, Eurofins Viracor: Employee Jerod Davidson, n/a, Eurofins Viracor: Employee Scott Cowden, MS, MB ASCP(CM), Eurofins Viracor: Employee Jamie Nutt, n/a, Eurofins Viracor: Employee
624. Outbreak of Human Trichinellosis Linked to Bear Meat Infected with Multiple Trichinella Species — Arizona, Minnesota, and South Dakota, 2022
Authors: Cash-Goldwasser Shama , Ortbahn Dustin , Narayan Muthu , Fitzgerald Conor , Maldonado Keila , Maldonado Keila , Maldonado Keila , Straily Anne , Sapp Sarah , Watson Billy , Qvarnstrom Yvonne , Margaret Neja , Berman David , Park Sarah Y , Smith Kirk , Holzbauer Stacy 
Published: November 2023

Abstract

Background
In July 2022, the Minnesota Department of Health was notified of a patient with fevers, myalgias, periorbital edema, and eosinophilia; providers suspected trichinellosis. Human trichinellosis is rare in the United States and usually acquired from wild game meat. We investigated to confirm the diagnosis, ascertain additional cases, and identify the source of infection.

Methods
Trichinellosis was defined as compatible symptoms in a person who consumed an epidemiologically implicated meal (probable) or had Trichinella antibodies (confirmed). Blood samples from exposed persons were tested for Trichinella antibodies and with unbiased sequencing for microbial cell-free DNA. Microscopy and a parasite detection assay based on deep sequencing were performed on suspected source meat.

Results
One week before symptom onset, the patient and 8 relatives from 3 states shared a meal including meat from a bear harvested in Saskatchewan, Canada. The meat was frozen for 5 weeks until being grilled with vegetables and served rare. There were a total of 6 cases (4 probable and 2 confirmed, attack rate = 75%). Six persons had a trichinellosis-compatible illness, of whom five submitted samples for Trichinella antibody testing and two had positive results. Plasma samples from the two antibody-positive patients were tested for microbial cell-free DNA, and both were positive for Trichinella spp. DNA. Motile Trichinella species larvae ( &gt;800 larvae per gram) were identified in bear meat frozen for 4 months. Deep sequencing detected 3 Trichinella genotypes, 2 of which matched reference sequences for T. nativa and Trichinella T6. The third genotype did not match any reference sequence; the closest match (94%) was Trichinella T9, which has only been detected in Japan.

Conclusion
We used multimodal diagnostic testing to characterize an outbreak of human trichinellosis and confirm bear meat as the source. Freezing kills Trichinella species commonly implicated in pork-associated outbreaks, but T. nativa and Trichinella T6 are freeze-resistant. Consumers of wild game meat should be informed that adequate cooking is required to kill Trichinella parasites. Further work on identification and classification of Trichinella species in North America is needed.

Disclosures
David Berman, DO, Precision Health Solutions, St. Petersburg, Florida: Advisor/Consultant
626. Antibiotic Stewardship Practices in hospitalized patients with Dengue in South India
Authors: Balasubramaniam Aishwarya , Dorairajan Sureshkumar , Chellapandian Yogavigneshwaran 
Published: November 2023

Abstract

Background
Antibiotics are commonly prescribed for upper respiratory viral infections, including COVID–19 infections worldwide. However, in the developing world, tropical viral infections like dengue, chikungunya, and zika are common causes of hospitalization throughout the year. But antibiotic prescribing behaviors for these infections were not studied well. Here, we are reporting the antibiotic prescribing practices for hospitalized patients with dengue in South India.

Methods
We conducted a retrospective analysis during the period of October 2022 to April 2023 at multiple tertiary care hospitals, involving serologically confirmed dengue (NS-1 antigen positive) fever patients in South India. Demographic data, laboratory parameters, antibiotic prescribing practices, supportive care treatment like papaya leaf extract tablets, and antibiotics on discharge were recorded using an audit tool. Descriptive statistics were used to analyze the data and the results were tabulated.

Results
During the study period 298 patients were admitted with confirmed dengue fever, other findings are listed in Table 1

Conclusion
Antibiotics were prescribed to 44% of hospitalized dengue patients and 41% of the patients were discharged with antibiotics. Doxycycline and cefixime were commonly prescribed antibiotics for the patients. Most (72%) of the dengue patients were receiving papaya leaf extract as a platelet-stimulating agent despite no evidence. In the future, antimicrobial stewardship practices in the developing world should focus on tropical infections apart from bacterial and fungal infections.

Disclosures
All Authors: No reported disclosures
630. SARS COV-2 genomic surveillance in Pakistan, an innovative approach
Authors: Ahmad Saeed , Idrees Fahmeeda 
Published: November 2023

Abstract

Background
Novel strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)harboring diverse gene mutations have periodically emerged and are spreading globally. Importantly, mutations within the spike gene's receptor-binding domain (RBD)are linked to SARS-CoV-2 transmissibility, disease severity, or decreased diagnostics vaccine efficacy. To identify SARS-CoV-2 variants rapidly,

Methods
we used a single primer-based PCR method in conjunction with Sanger sequencing. We focused on a region of the spike gene's RBD and S2 domains that contained lineage-defining mutational combinations.

Results
The genetic data obtained showed that delta and omicron subvariants were prevalent in the Khyber Pakhtunkhwa (KPK) region from January to February2022. Our survey found the highest prevalence of SARS-CoV-2 in the city of Peshawar (5.2%), followed by the districts of Mardan (1.8%), Karak (1.4%), Malakand(0.6%), and other districts.

Conclusion
We recommend that SARS-CoV-2 be monitored continuously to detect single-nucleotide polymorphisms (SNPs) that are causally linked to the emergence of new lineages. In resource-constrained settings, our method provides a rapid and cost-effective detection assay for SARS-CoV-2.

Disclosures
All Authors: No reported disclosures
633. Nanopore Sequencing and In-house Bioinformatic Pipeline for Rapid and Accurate Detection of NRTI, NNRTI, PI, and INSTI Drug Resistance Mutations
Authors: Salvaña Edsel Maurice , Arevalo Geraldine M , Dungca Niña Theresa , Alpay Riacarl , Schwem Brian 
Published: November 2023

Abstract

Background
Sanger-based sequencing (SBS) remains the gold standard for HIV-1 drug resistance testing (DRT). However, SBS output is still limited to an approximately 800-1000 bp read length. This is inadequate for amplifying the pol gene region that contains most of the clinically significant drug resistance mutation (DRM) positions, requiring separate steps for the protease (PR) and reverse transcriptase (RT) regions as is available in most commercial genotyping kits. Integrase (IN) gene is typically not sequenced, a major drawback since the WHO-recommended first-line treatment is now IN strand transfer inhibitor-based. We explore an alternative workflow for HIV-1 genotyping and DRT using the MinION sequencer to sequence a ∼2,800 bp amplicon covering PR and RT, and the first 224 codons of the IN region. This workflow also aims to reduce the turnaround time and cost of DRT.

Methods
Thirty samples (VL 3,160-3,520,000 copies/mL) previously tested for drug resistance underwent PCR amplification using customized primers targeting the pol gene. Agarose gel electrophoresis and library preparation (SQK-RBK110.96 kit, Oxford Nanopore Technologies) were then performed, followed by MinION sequencing. An in-house bioinformatic pipeline was used to analyze the sequencing data.

Results
MinION sequencing was able to detect all DRMs detected by SBS in all 27 samples and did not detect any DRMs in the ones without DRMs on SBS. A few additional DRMs undetected by SBS were detected by MinION sequencing which is expected since MinION is known to have higher minority variant sensitivity. Comparison of the resistance profiles showed that SBS and MinION sequencing are concordant with a kappa value of 95.8 interpreted as having perfect agreement (Landis & Koch, 1977). DRMs from IN could not be properly evaluated due to lack of positive SBS controls but will be assessed at a later time using deep-sequenced controls. The entire workflow from RNA extraction to data analysis for all samples was completed within 22 hours, significantly shorter than that of the WHO protocol for HIV-1 DRT. The projected cost per run is comparable with that of SBS with a more rapid turnaround time.

Conclusion
Our findings show that MinION sequencing and our in-house analysis pipeline can rapidly and accurately detect DRMs in HIV-1 positive patients.

Disclosures
Edsel Maurice Salvaña, MD, MSD: Advisor/Consultant|Pfizer: Advisor/Consultant
640. Efficacy of the Use of Bacteriophages to Combat Pectobacterium atrosepticum
Authors: Fabris Ian N , Kingett Melanie 
Published: November 2023

Abstract

Background
This inquiry aimed to investigate the potential of bacteriophages vB_PatP_CB3, vB_PatP_CB4, and vB_PatP_CB5 as methods for controlling the spread of Pectobacterium atrosepticum, a bacterial pathogen that causes black-leg disease and extensive crop damage.
Structure of Podovirus
Morphology of typical N4-like podovirus (Anatomy of an N4-like Podovirus phage, (adapted from Insight into DNA and Protein Transport in Double-stranded DNA Viruses: The Structure of Bacteriophage N4, J. McPartland, et al.))
Soft Rot in Potato
Pectobacterium atrosepticum infection in potato (Pectobacterium atrosepticum infection in Solanum tuberosum, the common potato (M. Kuznetsova All-Russian Institute of Phytopathology))

Methods
Phages were initially selected based on the location of isolation of the phage and its proximity to a field with a known current, or recent previous, Pectobacterium atrosepticum infection among potato crops. Phages were narrowed down by the specificity of their receptor-binding proteins for the protein receptors on the bacterium cell wall, as determined by FASTA sequence comparison between phage tail fiber RBPs and bacterial integral glycoproteins. A standard serial dilution and phage titration protocol in conjunction with a plaque assay were subsequently used to evaluate the efficacy of each phage, both individually and in a cocktail.
Plaque Assay Diagram
Standard plaque assay procedure used inoculate plates to obtain plaques

Results
Plaque assays showed that vB_PatP_CB5 produced a large number of plaques, indicating successful cell lysis and bacteriophage propagation within the bacterial colony. In contrast, vB_PatP_CB3 and vB_PatP_CB4 produced no measurable plaques.
Plaques on Bacterial Lawn
Observed plaque formation after initial 24 hour period
Plaque Charts from Trial 1
Plaque formation from trial 1
Plaque Charts from Trial 3
Plaque Charts from Trial 3

Conclusion
Based on these findings, it was concluded that vB_PatP_CB5 is the most effective at lysing and controlling growth of P. atrosepticum. These results have implications for the development of new phage-based treatments for black-leg disease and for limiting the associated crop damage.

Disclosures
All Authors: No reported disclosures
645. " Risk of Disease Severity and Disease Outcomes with Serotype-Specific Dengue Virus among Hospitalized Dengue Patients in a Tertiary Infectious Diseases Hospital: A Five-Year Retrospective Study"
Authors: San Diego Micaela J , SAYO A N A R I A A , EDRADA E D N A M 
Published: November 2023

Abstract

Background
Dengue fever is a significant cause of morbidity throughout the world caused by the dengue virus (DENV). Four antigenically different dengue virus serotypes (DENV-1,2,3, and 4) are known to cause infections in humans (Halsey,2012). Chances for developing dengue hemorrhagic fever-dengue shock syndrome increases significantly with history of previous infection with one of the four serotypes.

Methods
A retrospective study of hospitalized dengue patients in span of five years was done. One-hundred forty three (143) patients aged
&gt;19 years admitted due to fever, positive for NS1 antigen and with DENV serotype results were included. Clinical data were extracted from medical records including demographics, co-morbidities, clinical presentation, laboratory investigations, length of hospital stay and outcome.

Results
Out of the 143 adult dengue patients, the most prevalent serotype was DENV 3 at 64.34% followed by DENV 2 (18.18%), DENV 1 (11.19%), with DENV 4 as the least prevalent serotype (6.29%). In terms of clinical manifestations, the most prevalent symptoms were fever (98.60%), myalgia (78.32%), body malaise (69.23%), headache (59.44%), nausea and vomiting in 42.66%. Majority tested positive for Dengue NS1 (87.94%), with more than half testing positive for Dengue IgG at 54.24%. The adjusted risk for dengue with warning signs for DENV-2 was 5.94, indicating that the risk of dengue with warning signs was 5.94 times higher among those with DENV 2 than those with DENV 1; however, the association was not statistically significant. Results showed that the ARR for serotypes 3 and 4 for all dengue severity categories were not statistically significant (p&gt;0.05). The clinical outcome of patients was recovery at 98.60%, with only 1.40% mortality. Comparative analyses indicated that the clinical management and outcomes of the patients did not significantly differ according to dengue virus serotype (p&gt;0.05).

Conclusion
This study provided more information on the dengue serotypes, its effect on severity and outcome of the disease. Infecting dengue serotype play an important role in disease severity among adult dengue patients in the Philippines.

Disclosures
All Authors: No reported disclosures
649. Expansion Of A Low-Cost, Open-Source, Saliva-Based PCR Test For The Detection Of Mpox Virus
Authors: Thomas Russell , Yolda-Carr Devyn , Steel Sydney A , Tobik Emily R , Zepeda Theresa , Brownlee Maurice , Saladi Shyam , Parkin James , Fajardo Katherine , Allicock Orchid M , Wyllie Anne L 
Published: November 2023

Abstract

Background
Clinical diagnosis of mpox (monkeypox) virus relies on lesion swabs. Many patients experience prodromal symptoms prior to lesion-onset. Earlier detection could bolster outbreak response by mitigating transmission and facilitating access to antiviral treatments. With a growing number of studies reporting mpox detection in saliva, we adapted our saliva-based, extraction-free PCR test developed for SARS-CoV-2, for the detection of mpox virus.

Methods
We first compared five PCR assays for their detection of mpox DNA extracted from 30 saliva specimens collected into Spectrum SDNA-1000 tubes. Next, we investigated the stability of mpox detection in five raw, unsupplemented saliva samples diluted 1:5 in mpox-negative saliva, after storage at 4°C, ∼19°C (room temp.), 30°C, and 40°C for 72 hours. We also examined the stability of virus detection in three samples as per the FDA guidance for shipping of samples for testing. Additionally, we performed amplicon sequencing on 10 saliva samples and assessed concordance of the PCR assays against mpox virus sequences.

Results
The Logix Smart™ Mpox (2-Gene) RUO (Co-Diagnostics, Inc.) performed better at detection. Despite identifying three different substitutions in the CDC’s Monkeypox Virus Generic Real-Time PCR Test’s primers, results from ANOVA did not suggest a mean difference in cycle threshold values between assays. Detection following storage at 4°C, ∼19°C, and 30°C remained relatively stable for 24-48 hours but this declined by 72 hours. At 40°C, detection was stable at 24 hours but declined by 48 hours. Detection following simulated summer and winter shipping temperature profiles also remained stable.

Conclusion
Findings of this pilot investigation support a flexible, extraction-free, saliva-based PCR test as a promising approach for the low-cost detection of mpox virus. With stability observed for 24-48 hours as well as over simulated shipping temperatures, saliva-based sampling and simplified testing could reduce mpox diagnostic costs, increase access to testing and address hurdles in low- and middle-income countries. Future studies should assess the temporal dynamics of mpox virus in saliva.

Disclosures
Shyam Saladi, n/a, Neelyx Labs: Ownership Interest|SalivaDirect Inc: Board Member James Parkin, PhD, Neelyx Labs: employee Anne L. Wyllie, PhD, Co-Diagnostics: Board Member|Merck: Grant/Research Support|Pfizer: Advisor/Consultant|Pfizer: Grant/Research Support
652. Foodborne outbreak investigation at a wedding event – Batken, Kyrgyzstan, June 2022
Authors: Dautov Timur , Kemelbek Nasyat , Malisheva Marina , Otorbaeva Dinagul , Horth Roberta , Nabirova Dilyara 
Published: November 2023

Abstract

Background
On August 2nd, 2022, local health departments were informed that over a hundred people had sought care or reported gastrointestinal illness after attending the same wedding event in Batken, Kyrgyzstan, on July 30th. We investigated to identify the source and associated risk factors to stop transmission.

Methods
Using a retrospective cohort study design, we interviewed consenting wedding participants. A case was anyone who was linked to the event who became acutely ill or sought medical care with food poisoning symptoms. We searched public health surveillance records for additional cases who sought healthcare for suspected foodborne disease, a reportable illness, from July 30th to August 2nd. Food and environmental samples were collected and tested. We used logistic regression to determine associations with case status.

Results
Of 250 attendees, 201 consented; 110 were cases and 91 non-cases. Among cases, 8%were &lt; 20 years old, 27% were &gt;61 years old, and 80% were female. Top symptoms were fatigue (96%), abdominal pain (95%), diarrhea (95%), and fever (84%). Most cases developed symptoms &lt; 24 hours of the event and 79% sought care. Odds ratio was 7.8 for egg salad containing chicken (95% confidence interval [CI]: 4.1-14.4, p&lt; 0.01), 5.1 for grilled chicken (CI: 2.8-9.4, p&lt; 0.01) and 3.9 for chicken salad (CI: 2.2-7.1, p&lt; 0.01). Attack rate was 66% (105/160) among people who ate any chicken (95% of cases and 60% of non-cases). Patients were not tested. Proteus vulgaris, Klebsiella spp., and Escherichia coli were detected in chicken samples. E. coli was detected in 3/32 environmental samples.

Conclusion
Contaminated chicken was the likely source of illness. Source pathogen is uncertain because patients were not tested. Symptoms and onset were more consistent with Klebsiella spp. than E. coli, but Klebsiella spp food-associated outbreaks are rare. Recommendations were made to ensure restaurant compliance with food safety measures. Diagnostic testing for gastrointestinal illness needs strengthening.

Disclosures
All Authors: No reported disclosures
658. Oral Vancomycin Taper for First Occurrence of Clostridioides difficile Compared to Standard of Care: An Observational Retrospective Matched Cohort Study
Authors: Moore Sarah E , Swingler Elena A , Song Matthew , Wilde Ashley M 
Published: November 2023

Abstract

Background
Clostridioides difficile infection (CDI) recurrence rates may be reduced with fidaxomicin, but financial barriers can limit access. Tapered and/or pulsed oral vancomycin is recommended in patients with recurrent CDI, however there is currently limited data for use in treating initial CDI.

Methods
Multicenter retrospective propensity-matched cohort study in patients ≥ 18 years old hospitalized with a first occurrence of CDI from 6/18/2018 – 12/21/2021 conducted at Norton Healthcare in Louisville, Kentucky. Standard of care (SOC) was receipt of oral vancomycin for 10-14 days compared to a standardized oral vancomycin taper (Figure 1). Subjects were matched based on age &lt; or ≥ 65 and receipt of non-CDI antibiotics during index hospitalization or within 6 months post-discharge. Selected baseline characteristics and receipt of CDI and non-CDI antibiotics were collected. Non-CDI antibiotics were stratified by high, medium or low risk for CDI. The primary outcome was CDI recurrence within 6 months of hospital discharge. Secondary outcomes included time to recurrence, recurrence rates stratified by age group &lt; or ≥ 65 years, CDI severity of illness per IDSA guidelines and all-cause mortality within 6 months of hospital discharge. Categorical variables were analyzed using Chi-squared and Fisher’s exact tests as appropriate.
Standardized Oral Vancomycin Taper

Results
Recurrence rates at 6 months were 5.3% (4/75) in the taper arm and 28% (21/75) in the SOC arm (p=0.002). All-cause mortality was 20% (15/75) in the taper arm and 5.3% in the SOC arm (p=.026). Severe/fulminant CDI occurred in 49.3% of the taper arm and 58.7% of the SOC arm (p=0.53). Both groups received antibiotics at the same rate based on matching, and rates of antibiotics considered high risk for CDI were similar at 65% in the taper and SOC groups (65% vs. 61.3%, p=0.809). More patients in the taper arm were immunocompromised (25.3% vs 9.3%, p=0.029).

Conclusion
A significantly lower rate of CDI recurrence was observed at 6 months with tapered oral vancomycin coupled with higher all-cause mortality in patients being treated for first CDI. Additional information is needed to elucidate the clinical utility of this approach.

Disclosures
Ashley M. Wilde, PharmD, BCIDP, Pfizer: Grant/Research Support